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(hide) 23andMe/SNPs
homozygous for C677T of MTHFR = 10-20% efficiency in processing folic acid = high homocysteine, low B12 and folate levels This is the homozygous form of the C677T allele for the MTHFR gene. It is found in approximately * 15% of Hispanic Americans * 12% of Caucasian Americans * 12% of Japanese * 6% of Germans * 3% of Asians * 2% of African Americans * 1% of Sub-Saharan Africans Numerous health effects are associated with this variant. * Hyperhomocysteinemia and neurologic disorders: a review. (2014). A review. Certain genetic factors also cause elevated homocysteine levels, such as C667T substitution of the gene encoding methylenetetrahydrofolate reductase. Elevated homocysteine has been observed in several medical conditions, such as cardiovascular disorders, atherosclerosis, myocardial i...
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer ** renal cancer * cleft lip and cleft palate * coronary artery disease * dementia * depression * hyperhomocysteinemia * migraine * neural tube d...
watch out for high fat in diet
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rs1801282, also known as Pro12Ala, is a common SNP in the peroxisome proliferator-activated receptor PPARG gene. The more common (C) allele (in dbSNP orientation) encodes the 'Pro' amino acid at this SNP position. rs1801282 has been reported to be associated with metabolic syndrome, but other studies have not been able to replicate any strong or significant effect. The association between type-2 diabetes and SNP rs1801282 is mentioned as being replicated in rs1801282 and risk of cognitive decline in elders? Maybe with diabetes. A ten-year study of 679 male patients with symptomatic coronary artery disease found that rs1801282(G) carriers had a much lower (10 year) cardiovascular risk, with the hazard ratio estimated to be 0.10 (CI: 0.01-0.70, p = 0.02) for ischemic heart disease and 0.24 f...
A1/A2: Bad at avoidance of errors. 0.5x lower OCD risk, 0.87x lower Tardive Diskinesia risk, higher ADHD risk. More Alcohol Dependence. Lower risk of Postoperative Nausea. Increased obesity. Bupropion is not effective. The DRD2 TaqIA A1/A2 version causes less dopamine receptors. Doesn't learn from mistakes well. Reduced response to errors and increased addictive behavior Men may have half the risk of Obsessive Compulsive Disorder but higher risk of ADHD. Women have lower Persistence. 0.87x reduced risk of Tardive Diskinesia when taking dopamine receptor antagonists. Slightly increased risk of alcoholism and smoking addiction. Slower recovery from traumatic brain injury. Lower risk of postoperative nausea within 6 hours of surgery. Bupropion (Wellbutrin, Budeprion, Prexaton, Elontril, Aple...
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rs1800497, a SNP also known as the TaqIA (or Taq1A) polymorphism of the dopamine D2 receptor DRD2 gene (even though it is actually located over 10,000bp downstream of the gene), gives rise to the DRD2*A1 allele. This allele (rs1800497(T)) is associated with a reduced number of dopamine binding sites in the brain . Reduced response to errors and increased addictive behavior It has been postulated to play a role in alcoholism, smoking, and certain neuropsychiatric disorders. The reduced number of dopamine binding sites may play a role in nicotine addiction by causing an 'understimulated' state that can be relieved by smoking (and/or use of other drugs). A wide variety of reports have been published over more than ten years either linking rs1800497 to aspects of nicotine use and smoking cessa...
1.3x risk of prostate cancer; aspirin reduces risk of colorectal cancer Increased risk for prostate cancer and in women other types of cancer. Aspirin has been reported to help reduce the risk somewhat when taken by carriers of this genotype.
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rs6983267 is a SNP on chromosome 8q24, associated with increased risk for several cancers, particularly prostate cancer. In studies dividing the 8q24 region, this SNP falls in region 3. This SNP has also been reported to influence the cancer-risk-decreasing effect of aspirin. In a study of over 3,600 Caucasians with prostate cancer, rs6983267 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On their own, the rs6983267(G;G) and (G;T) risk genotypes yield an odds ratio for developing prostate cancer of 1.37 (CI: 1.18-1.59, p=3.4-10e-5) and may account for 22.2% of population attributable risk. The increased risk of developing prostate cancer associated with rs6983267 now appears to be independent of the risk associated with its close neig...
Increased risk of Atrial Fibrillation in one of the 2 SNPs mentioned by 23andMe.
The more important of the two atrial fibrillation SNPs mentioned by 23andMe has one defective copy. This slightly affects the formation of the heart and increases risk of Atrial Fibrillation (quivering of the top part of the heart) that 23andMe reports. It also seems to increase the risk of Cardioembolic ischemic stroke (blocked blood flow to the brain) although 23andMe doesn't mention that. The risk is highest for men. Based on several quality studies, and confirmed for Europeans and Asians. It's recommended to eat a heart-healthy diet, and only drink alcohol in moderation, to lower the risk.
3.08x chance of developing primary biliary cirrhosis
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23andMe blog *Each G at rs2856683 increased the odds of primary biliary cirrhosis by 1.75x. *Each G at rs6441286 increased the odds of primary biliary cirrhosis by 1.54x. *Each A at rs3790567 increased the odds of primary biliary cirrhosis by 1.51x. [PharmGKB:Curated A GWAS of 2072 Canadian and U.S. subjects (536 patients with primary biliary cirrhosis and 1536 controls) showed that primary biliary cirrhosis was significantly and reproducibly associated with this SNP (rs6441286) at the IL12A locus (P=2.42x10(-14); odds ratio, 1.54).] [OMIM:?] [GWAS:Primary biliary cirrhosis]
1.3x risk of rheumatoid arthritis; 1.55x risk of SLE; 1.42x risk of Sjögren's syndrome; increased risk of type-1 diabetes; and increased risk of primary biliary cirrhosis.
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rs7574865, a SNP in the third intron of the STAT4 gene, has been reported in a large study of Swedes to be associated with both rheumatoid arthritis (RA) and lupus (SLE). Among other studies, it has been confirmed in a meta-analysis of 8 studies totaling 7,381 patients and over 10,000 controls from both European and Asian populations. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated the presence of a risk allele was 1.3 for rheumatoid arthritis and 1.55 for lupus (SLE). The paper states that, 'Homozygosity of the risk allele, as compared with absence of the allele, was associated with a more than doubled risk for lupus and a 60% increased risk for rheumatoid arthritis.' A study of 124 Caucasian patients with primary Sjögren's syndrome, an autoimmune dise...
2.6x increased thyroid cancer risk
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Each A at rs965513 increased the odds of thyroid cancer by 1.75 times. Each T at rs944289 increased the odds of thyroid cancer by 1.37 times. A genoset, Gs137, has also been created in SNPedia to represent the increased risk reported for carriers of both variants. See also: 23andMe blog [PharmGKB:Non-Curated GWAS results: Common variants on 9q22.33 and 14q13.3 predispose to thyroid cancer in European populations. (Initial Sample Size: 192 cases, 37,196 controls; Replication Sample Size: 432 cases, 1,727 controls); (Region: 14q13.3; Reported Gene(s): NKX2-1; Risk Allele: rs944289-T); (p-value= 0.000000002).This variant is associated with Thyroid cancer.] [OMIM:THYROID CARCINOMA, PAPILLARY]
Mix of muscle types. Likely sprinter. Normal for white people. One working and one defective copy of the gene for alpha-actinin-3 in fast-twitch muscle fibres. This genotype may indicate somewhat impaired muscles, however many sprinters and some endurance athletes have this.
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This SNP, in the ACTN3 gene, encodes a premature stop codon in a muscle protein called alpha-actinin-3. The polymorphism alters position 577 of the alpha-actinin-3 protein. In the (C;C) genotype is often called RR. The truncated (T;T) is often called XX. (T;T) is under-represented in elite strength athletes, consistent with previous reports indicating that alpha-actinin-3 deficiency appears to impair muscle performance. The most common nucleotide at this position, (C), encodes an arginine (amino acid code R), the alternative T allele encodes a stop codon (X). Hence, the SNP is referred to as R577X, with homozygotes being either RR or XX and heterozygotes being RX. XX individuals completely lack the expression of alpha-actinin-3. An earlier report studying a relatively small number of Austr...
0.61x reduced risk of Male Pattern Baldness. Discovered by 23andWe based on customer surveys, and considered preliminary research.
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This is the 23andWe discovery: 'Male Pattern Baldness: Preliminary Research'. It affects appearance.
1.28x increased Basal Cell Carcinoma risk. Increased risk of this kind of skin cancer. This is the most common kind of cancer in the United States. This kind has less danger of metastasizing, but still needs to be treated if it occurs. Note that if you have both the Basal Cell Carcinoma mutations, your combined risk would be 2.68x.
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2 SNPs located in different regions of chromosome 1 are likely to be associated with increased risk for basal cell carcinoma (BCC), the most common form of skin cancer. *each A at rs7538876 yields a 1.28x increased risk of developing BCC (p = 4.4 x 10e-12) *each G at rs801114 also yields a 1.28x increased odds of developing BCC (p = 5.9 x 10e-12) *2.68x increased risk of BCC for homozygous carriers of both SNPs This study was based on an analysis of ~2,000 Icelandic and Eastern European skin cancer patients (as well as a large number of controls). The authors estimate that approximately 1.6% of all individuals of European ancestry are homozygous for both risk alleles, and thus that percentage of the population is at 2.68x higher risk for BCC compared to individuals who are rs7538876(G;G) a...
increased risk for heart disease
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discussed in this blog post as possibly playing a role in coronary heart disease This SNP was also associated with increased risk for coronary artery disease in a Korean population. The association remained significant after adjusting for significant clinical covariates (P=0.001 to 0.024). We identified one risk haplotype (GGGG; P=0.017) and one protective haplotype (AAAA; P=0.007) for development of CAD. Further analysis suggested that the SNPs probably confer susceptibility to CAD in a dominance model (covariates-adjusted P=0.001 to 0.024; OR=2.37 to 1.54). Also found to be significant in a study of 416 Italian myocardial infarction patients. Found to be associated with coronary heart disease in a study of 1360 Chinese Han patients, with an odds ratio of 1.52 (CI: 1.13 - 2.04) for rs2383...
Avg. fasting Plasma Glucose 5.18 mmol/L (93 mg/dl). Slightly higher blood glucose. Fasting Plasma Glucose is the amount of sugar in your blood when you wake up. It's required to power your body, but too much is very bad for you. Fasting plasma glucose between 5.6 mmol/L and 6.9 mmol/L (101 – 125 mg/dl) is considered pre-diabetes. Fasting plasma glucose higher than 7 mmol/L (126 mg/dl) is considered diabetes.
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rs560887, p = 4 x 10(-7)) *654 normoglycemic subjects, replicated in 9,353 subjects *fasting plasma glucose (FPG) (beta = -0.06 mmol/l per A-allele, combined p = 4 x 10(-23)) and with pancreatic beta-cell function (Homa-B model, combined p = 3 x 10(-13)) in three populations; however it was not associated with type 2 diabetes risk. (ageing) Blood Glucose [PharmGKB:Non-Curated Phenotype 1: In a meta-analysis of 21 GWAS cohorts followed by analysis in additional individuals, this SNP was found to be associated with fasting glucose level. Study size: 119,169. Significance metric(s): p = 8.7 x 10(-218). Phenotype 2: In the same study, this SNP was found to be associated with HOMA-B (homeostasis model assessment of beta-cell function). Study size: 94,839. Significance metric(s): p = 1.5 x 10(-...
Carrier of one CYP1A2*1F allele; Slow Caffeine Metabolizer. One copy of the slow caffeine metaboliser SNP, and one copy of the fast version. This makes you more strongly affected by drinking coffee, as caffeine is broken down slower in the liver. Supposedly this increases the risk of heart attacks, although other studies show caffeine is generally good for the heart. It also makes caffeine more effective at preventing Breast Cancer, Alzheimer's Disease, and Parkinson's disease. Too much caffeine will shrink your breasts.
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rs762551, also known as -164A>C or -163C>A, is a SNP encoding the CYP1A2*1F allele of the CYP1A2 gene. For historic reasons, the rs762551(C) allele is considered the wild-type, even though it is the rarer allele in most populations. The rs762551(A) allele is the 'fast metabolizer' allele known as CYP1A2*1F; the (C) allele is by comparison a slower metabolizer of certain substrates (including caffeine). In terms of genotypes, only rs762551(A;A) individuals are considered fast metabolizers. Individuals who are rs762551(A;C) heterozygotes or rs762551(C;C) homozygotes are both considered slow metabolizers. The CYP1A2 gene encodes a member of the cytochrome p450 family of proteins, which metabolize nutrients and drugs. One well known substrate of CYP1A2 is caffeine; individuals who are ca...
Normal risk of sexual dysfunction when taking SSRI Antidepressants.
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rs6311 (-1438A>G / A-1438G or -1438G>A / G-1438A) is a SNP located upstream (and within the promoter region of) HTR2A. Multiple Regulatory Variants Modulate Expression of 5-Hydroxytryptamine 2A Receptors in Human Cortex. The minor A allele of rs6311 reduces expression of a previously unannotated extension of the 5' untranslated region of HTR2A mRNA. rs6311 together with rs6314 have a modest effect on depression severity, when examined in the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study. Three (rs643627-rs594242-rs6311: A-C-T), two (rs594242-rs6311: C-T) and a single functional (rs6311: T) marker were protective against suicidal behavior. The complementary markers (rs594242-rs6311: G-C and rs6311: C) were associated with increased risk for non-violent and impu...
Magnitude: 2
Frequency: 7.1%
Repute:Bad
References:14
Frequency: 7.1%
Repute:Bad
References:14
1.5x increased bladder cancer risk
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rs9642880 is a SNP located in chromosome region 8q24, a region that has been linked to prostate, breast, and colon cancer. A study ultimately totaling over 4,000 bladder cancer patients of European ancestry (and 40,000 controls) concluded that individuals carrying two copies of rs9642880(T) were at 1.49x increased risk (allele-specific odds ratio = 1.22, p = 9 x 10e-12) for the disease. This SNP was not associated, however, with risk for prostate, breast, or colon cancer. Another study in Chinese populations found similar results in regard to bladder cancer. rs9642880(T;T) estimated risk of developing 1.49 times that of noncarriers. 1,803 urinary bladder cancer cases and 34,336 controls. No association with prostate, colorectal and breast cancers. In contrast to GSTM1 SNPs, the rs9642880(T...
Magnitude: 2
Frequency: 50.0%
Repute:Bad
References:77
Frequency: 50.0%
Repute:Bad
References:77
1.3x risk for Heart Attack. Normal risk for Abdominal Aortic Aneurysm and Brain Aneurysm. One copy of an SNP that increases risk of Myocardial Infarction (Heart Attack) and other Coronary Heart Disease. It has been shown that regularly eating raw vegetables and fruit can reduce the risk to the same level as people without this SNP. This SNP also has the normal medium risk of abdominal aortic aneurysm (weakened artery to abdomen and legs) or brain aneurysm (weakened artery to brain).
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This SNP, rs10757278, is one of several clustered together in a region of chromosome 9 that has been linked to increased risk for heart disease and potentially diabetes. The overall estimate of heart disease cases that may involve this SNP (or related ones nearby) is said to be 20-30%. The risk allele, rs10757278(G), shows an increased association for myocardial infarctions ('MI'; heart attacks) both in general and more specifically in so-called early onset MI. The odds ratio relative to rs10757278(A:A) 'noncarrier' individuals for rs10757278(G;G) individuals is 1.64 (CI: 1.47-1.82), and for carriers of one risk allele, i.e. rs10757278(A;G) individuals, 1.26 (CI: 1.16-1.36). For early onset MI, the odds are slightly higher; homozygote rs10757278(G;G) individuals have an odds ratio of 2.02 ...
1.4x increased risk of Atrial Fibrillation and ischemic stroke. One defective copy. This affects the formation of the heart and gives a higher risk of Atrial Fibrillation (quivering of the top part of the heart), and Cardioembolic and Ischemic strokes (blocked blood flow to the brain). Based on several quality studies, and confirmed for Europeans and Asians. It's recommended to eat a heart-healthy diet, and only drink alcohol in moderation, to lower the risk.
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Two SNPs from chromosome 4q25, rs2200733 and rs10033464, were found to be associated with atrial fibrillation in a study of both European and Asian populations. The odds ratio associated with one or more copies of either risk allele was ~1.4x. The results derived from a study of 78 Italians with atrial fibrillation (AF) and atrial flutter (AFL) agree with previously reported findings from the Icelandic study (), which also found that the rs2200733(T) was associated with AF/AFL disease. In 1,661 Icelandic ischemic stroke samples and two large European replication sets combined, rs2200733 was associated with cardioembolic stroke (CES) (odds ratio 1.54, p = 8.05 x 10e-9). rs2200733 even showed association to ischemic stroke that was not classified as cardioembolic stroke. rs2200733 and rs1003...
Normal risk of Atopic Dermatitis. This seems to be a proxy that 23andMe uses for the filaggrin gene variants that they can't measure directly.
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Atopic Dermatitis
Back Pain: lower risk of Lumbar Disc Disease. This appears to reduce the risk of LDD, at least in Japanese people and women.
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The rs2073711 SNP (1184T→C ) is located in exon 8 of the cartilage intermediate layer protein gene (CILP). However, CILP gene is primarily known to be expressed abundantly in intervertebral discs, and was reported to have increased expression when degeneration occurs . For the rs2073711 SNP, the ancestral allele is T and the disease associated risk allele is C. A study of Asian patients with lumbar disc disease (LDD) implicates each copy of a (C) allele of SNP rs2073711 (as oriented with respect to dbSNP) as increasing risk about 1.6 fold. ==Background== Low back pain (LBP) is an enervating condition that affects 70-85% of all people during their lifetime . It can lead to decreased physical activity and quality of life, presenting considerable negative socioeconomic and health impact...
1.5x increased risk for Childhood Asthma.
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rs7216389, a SNP in the ORMDL3 gene on chromosome 17q21, was associated with susceptibility to childhood asthma in a study of ~1,000 British patients. The variation appears to be linked to altered levels of the ORMDL3 mRNA, which was shown in a cohort study of ~5,000 British and German patients to be correlated to childhood asthma. A large study of Scottish asthma patients replicated these results, finding that a single copy of the T allele conferred an odds ratio of 1.50 (CI: 1.24-1.81) and 2 copies conferred an odds ratio of 2.11 (CI: 1.71-2.61), respectively. [PharmGKB:Non-Curated GWAS Results: Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma (Initial Sample Size: 994 cases, 1,243 controls; Replication Sample Size: 2,320 cases, 3,301 controls; Ri...
4.6x increased risk of Ankylosing Spondylitis. Substantially increased (but still only 0.5%) risk of this rare autoimmune disease that causes inflammation of the spine and joints. Based on preliminary research. Age of onset is usually between 15 and 25, so if you are older than that, there's not much need for worry.
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Each A allele at rs7743761 is associated with 4.6x higher risk of ankylosing spondylitis, according to a 2007 publication. [GWAS:Ankylosing spondylitis]
2.3x risk of rheumatoid arthritis
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rs6457617 has been reported in a large study to be associated with rheumatoid arthritis. This SNP is reported to be the most statistically significant of many SNPs similarly located in the MHC region. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with heterozygotes is 2.36 (CI 1.97-2.84), and for homozygotes, 5.21 (CI 4.31-6.30). [GWAS:Rheumatoid arthritis]
Magnitude: 2
Repute:Bad
References:0
Repute:Bad
References:0
Normal (higher) risk of Asthma. This is normal for white people. But this (C;T) has 1.58x the risk compared to T;T (normal for non-white people). Tested in Koreans.
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Asthma
1.3x increased risk for multiple sclerosis
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The (C) allele of rs6897932, located in the alternatively spliced exon 6 of IL7RA gene and encoding the amino acid threonine rather than isoleucine at amino acid position 244, is associated with a slight increase (18%) in risk of developing multiple sclerosis. [PMID 17660817; Nature Genetics 39, 1083 - 1091 (2007) SG Gregory et al.] Note that the (C) allele is the most common at this position in all known populations and influences the ratios of the alternative isoforms (membrane bound and soluble) of the gene. blog post giving perspective on the significance of this snp a significant risk factor for multiple sclerosis in four independent (overall P = 2.9 x 10(-7)) influences the amount of soluble and membrane-bound isoforms of the protein by putatively disrupting an exonic splicing silenc...
Normal risk of Atopic Dermatitis.
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23andMe blog associated rs7927894(T) with Crohn’s disease 1.16x and atopic dermatitis [PharmGKB:Non-Curated GWAS results: A common variant on chromosome 11q13 is associated with Dermatitis, Atopic. (Initial Sample Size: 939 cases, 975 controls, 1,097 family members; Replication Sample Size: 2,637 cases, 3,957 controls); (Region: 11q13.5; Reported Gene(s): C11orf30; Risk Allele: rs7927894-A); (p-value= 0.0000000008).This variant is associated with Dermatitis, Atopic.] [OMIM:?] [GWAS:Atopic dermatitis]
Normal (higher) risk of Asthma.
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rs4950928 in CHI3L1 is likely to play roles in the predisposition to schizophrenia. An attempt to repeat the association between rs4950928 and risk for schizophrenia in an ethnically identical population (Japanese) as well as a new population (Han Chinese) failed to show any significant association. In contrast to previous studies, in this study of 6514 Danish adults the rs4950928(G) allele - rather than the (C) allele - was found to be associated with asthma. [PharmGKB:Non-Curated GWAS Results: Effect of Variation in CHI31 on Serum YKL-40 Level, Risk of Asthma, and Lung Function (Initial Sample Size: 632 individuals; Replication Sample Size: 206 children; Risk Allele: rs4950928-G). This variant is associated with YKL-40 levels.] [OMIM:CHITINASE 3-LIKE 1; CHI3L1] [GWAS:YKL-40 levels]
Normal risk of Basal Cell Carcinoma. Normal risk for this kind of skin cancer.
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2 SNPs located in different regions of chromosome 1 are likely to be associated with increased risk for basal cell carcinoma (BCC), the most common form of skin cancer. *each A at rs7538876 yields a 1.28x increased risk of developing BCC (p = 4.4 x 10e-12) *each G at rs801114 also yields a 1.28x increased odds of developing BCC (p = 5.9 x 10e-12) *2.68x increased risk of BCC for homozygous carriers of both SNPs This study was based on an analysis of ~2,000 Icelandic and Eastern European skin cancer patients (as well as a large number of controls). The authors estimate that approximately 1.6% of all individuals of European ancestry are homozygous for both risk alleles, and thus that percentage of the population is at 2.68x higher risk for BCC compared to individuals who are rs7538876(G;G) a...
~0.4cm taller 0.4cm taller than average
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nature SNP rs1042725 is associated with height (P = 4E-8) in a study involving over 20,000 individuals. The gene harboring this SNP, HMGA2, is a strong biological candidate for having an influence on height, since rare, severe mutations in this gene are known to alter body size in mice and humans. rs1042725 is estimated to explain approx 0.3% of population variation in height in both adults and children (approx 0.4 cm increased adult height per C allele). rs1042725 is associated with increased height (0.36 cm 95% IC[0.12-0.61] per C allele, P=0.004). in men rs1042725 may explain 3% of height variability [PharmGKB:Non-Curated GWAS Results: A common variant of HMGA2 is associated with adult and childhood height in the general population (Initial Sample Size: 4,921 individuals; Replication S...
Normal (higher) risk of Bipolar Disorder. This is the most common version of this SNP, so most people have this. But it is suspected of having a higher risk of Bipolar Disorder compared to the other rare versions of this SNP.
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Bipolar disorder failed to replicate in [PharmGKB:Non-Curated GWAS Results: A genome-wide association study implicates diacylglycerol kinase eta (DGKH) and several other genes in the etiology of bipolar disorder (Initial Sample Size: 461 cases, 563 controls; Replication Sample Size: 772 cases, 876 controls; Risk Allele: rs1012053-A).] [GWAS:Bipolar disorder]
Magnitude: 1.5
Repute:Bad
References:10
Repute:Bad
References:10
1.20x risk of developing ALS
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rs10260404, a SNP in the region of the DPP6 gene on chromosome 7, has been associated with the sporadic form of ALS (Lou Gehrig's disease) in a study of 1000+ European patients. The overall odds ratio for the risk allele rs10260404(C) is 1.30 (CI: 1.18-1.43, p=0.017). When broken down by genotype, the odds ratios for heterozygotes are 1.20 (CI: 1.06-1.41), and for rs10260404(C;C) homozygotes, 1.60 (CI: 1.32-1.92). A 'C-C' haplotype for this SNP and that of it's neighbor rs10239794 is also highly (statistically; p=10e-9) associated with ALS. However, in an expanded study pooling 4 populations (Irish, Dutch, US, Polish) rs10260404 failed to reach Bonferroni significance. although it did remain significant in the (expanded) Irish-only population. [PharmGKB:Non-Curated GWAS results: Screening...
Normal risk of developing bladder cancer. This is the normal risk of bladder cancer, particularly in Europeans and in people who already have tumors with low risk of progression.
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rs710521 is a SNP located in chromosome region 3q38, near the TP63 gene. A study ultimately totaling over 4,000 bladder cancer patients of European ancestry (and 40,000 controls) concluded that individuals carrying two copies of rs710521(A) were at 1.4x increased risk (allele-specific odds ratio = 1.19, p = 1 x 10e-7) for the disease. An additional 1,425 bladder cancer patients, supplemented by a meta-analysis of 5,695 additional cases (and 40,000+ controls), did replicate a (somewhat) increased risk associated with the rs710521(A) allele. The overall odds ratio was 1.18 (OR: 1.12 - 1.25, p < 0.0001). Another study in Chinese populations did not find an increased risk of bladder cancer for this SNP. [PharmGKB:Non-Curated GWAS Results: Sequence variant on 8q24 confers susceptibility to ...
Possibly reduced risk of Bipolar Disorder. This appears to lower the risk of Bipolar Disorder compared to the more common version of the gene, based on preliminary research.
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Linked to bipolar disorder in one of the most comprehensive studies in 2007. Risk allele with reference to dbSNP orientation is reported to be (T), with either one or two copies leading to an odds ratio of 2 (CI 1.6-2.7). Some replications, but in 2011 23andMe published as failed to replicate in Pharmacogenetics: data, concepts and tools to improve drug discovery and drug treatment. Findings from bipolar disorder genome-wide association studies replicate in a Finnish bipolar family-cohort. Simultaneous genotype calling and haplotype phasing improves genotype accuracy and reduces false-positive associations for genome-wide association studies. [PharmGKB:Non-Curated GWAS Results: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Initial Sample...
~1.5x increased risk for chronic lymphocytic leukemia
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rs872071 is a SNP associated with the interferon regulatory factor 4 IRF4 gene. In a GWAS study including over 1,500 Caucasian patients with chronic lymphocytic leukemia (CLL), the rs872071(G) allele showed the strongest association (p = 1.91 x 10e-20) of all SNPs studied. The reported odds ratio was 1.54. See also: 23andMe blog A subsequent study () has found a similar association extending to another 800+ Spanish and Swedish CLL patients. rs872071 was also seen to be associated with CLL in Hong Kong Chinese (71 patients), with a reported odds ratio of 1.78 (CI: 1.25-2.53). A related hematologic malignancy, Hodgkin's lymphoma, may also be influenced by rs872071. Two case-control series totalling 529 and 2192 patients found an odds ratio of 1.21 (CI: 1.05-1.39, p = 0.009). [PharmGKB:Non-C...
1.4x higher risk for Ankylosing Spondylitis. Higher, but still very low, risk (0.14%) of this rare autoimmune disease that causes inflammation of the spine and joints.
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rs30187 is one of several SNPs in the ERAP1 gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. Each T allele appears to increase the odds by about 1.4x (p=3.4x10e-10). A study of 872 Korean patients found that each T allele was associated with 1.5x higher odds of ankylosing spondylitis. [GWAS:None]
Magnitude: 1.4
Frequency: 37.2%
Repute:Good
References:9
Frequency: 37.2%
Repute:Good
References:9
0.71x lower risk for Ankylosing Spondylitis. Very low risk (about 0.07%) of the rare autoimmune disease that causes inflammation of the spine and joints. Based on preliminary research.
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rs10050860 is one of several SNPs in the ERAP1 gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 0.71 (p=7.7x10e-9). Note that the text description (but not the result) at 23andMe is wrong. It is the uncommon T allele that gives protection. Association of an ERAP1 ERAP2 haplotype with familial ankylosing spondylitis. Investigating the genetic association between ERAP1 and ankylosing spondylitis. Serum cytokine receptors in ankylosing spondylitis: relationship to inflammatory markers and endoplasmic reticulum aminopeptidase polymorphisms. ERAP1 polymorphisms and haplotypes are associated with ankylosing spondylitis susceptibility and functional severity in a Spanish population. Associations between ERAP1...
1.3x higher risk for glioma development
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23andMe blog rs2736100 C 1.27 Glioma Lung cancer susceptibility locus at 5p15.33. Common genetic variants on 5p15.33 contribute to risk of lung adenocarcinoma in a Chinese population. Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility. Deciphering the impact of common genetic variation on lung cancer risk: a genome-wide association study. Role of 5p15.33 (TERT-CLPTM1L), 6p21.33 and 15q25.1 (CHRNA5-CHRNA3) variation and lung cancer risk in never-smokers. Individuals susceptible to lung adenocarcinoma defined by combined HLA-DQA1 and TERT genotypes. New insights into susceptibility to glioma. Replication of lung cancer susceptibility loci at chromosomes 15q25, 5p15, and 6p21: a pooled analysis from the International Lung Cancer Consortium. Evaluatio...
possibly lower HDL cholesterol in women One report indicates that women (but not men) with this genotype may have slightly lower levels of HDL cholesterol, but other reports have not observed this.
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rs5370, also known as Lys198Asn or K198N, is a SNP in the endothelin-1 EDN1 gene on chromosome 6. The generally more common rs5370(G) allele encodes the Lys (K), and the rarer rs5370(T) allele encodes the Asn (N). Among the French-Canadian founder population of the Saguenay Lac St-Jean region of Quebec, rs5370(T) was associated with lower HDL cholesterol values in women (p = 1.3 x 10e-5), but not in men. In a study of 1,000+ Western Australians, no association was seen between HDL levels and rs5370. A study of ~400 rheumatoid arthritis patients found a 3x increase in the adjusted odds of being hypertensive for rs5370(T;T) homozygotes compared to (G;G) homozygotes (odds ratio 2.89, CI: 1.02 - 8.19, p=0.011). After adjustment for multiple potential confounders, haplotype analysis revealed an...
The (A;G) genotype averages 2.8 PIQ points higher than the (G;G), but averages 2.84 PIQ points lower than (A;A) genotype
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SNPs in the SNAP25 gene were initially linked to intelligence but have failed to replicate . While now suspect, the original work can be found in . The (A;A) genotype averaged 2.84 PIQ points higher than the (A;G) genotype, which averages 2.8 PIQ points higher than the (G;G) genotype (p=0.0002). Variance in this SNP may account for 3.4% of the phenotypic variance in PIQ. rs363050 is in close linkage with rs353016, with r2 = 0.98, such that the rs363050(A) allele typically is linked to the rs353016(T) allele. For SNPs rs363039 - rs363043 - rs353016, respectively, the haplotype C-T-T is most associated with higher intelligence in children, whereas the haplotype C-C-T is most associated in adults (SNPs oriented as in dbSNP). Measures of Intelligence
Can taste bitter. Normal tasting ability for bitterness. This makes turnip, cabbage, brussels sprouts, broccoli, and other cruciferous vegetables taste more interesting and less horribly bland. Coffee and dark beers also tastes more bitter. You can taste propylthiouracil (PROP), PTC, and related chemicals. On the other hand, you can't taste the unpleasant bitterness of the tropical fruit from the Bignay tree, it will taste sweet to you. You probably eat healthier.
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rs713598 is one of three SNPs that form the main haplotypes behind the ability to perceive as bitter the taste of the compound phenylthiocarbamide (PTC) and similar molecules in foods (like cabbage and raw broccoli) or drinks (like coffee and dark beers). The rs713598(G) allele, in the orientation shown in dbSNP, is the 'tasting' allele, and it is dominant to the 'non-tasting' allele rs713598(C), so having one copy is enough to have the bitter tasting ability. If you are a 'taster', you're also likely to carry at least one rs10246939(C) and one rs1726866(C) allele since, along with rs713598(G), these three SNPs form the most common tasting haplotype. If you lack these alleles, you're quite likely (~80%) to be a non-taster of bitterness, meaning that foods that may taste bitter to others ta...
2-6x increased risk for cluster headaches
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rs2653349, also known as G1246A, is a SNP in the HCRTR2 hypocretin-orexin gene. It has been linked primarily to cluster headaches. The more common allele (G) has been linked to increased risk; alternatively, this could be seen as implying that the less common (A) allele reduces cluster headache risk. In the (first) study, 100+ Italian patients were analyzed to reveal that rs2653349(G;G) genotypes were at 5x increased risk for the disorder, compared with (A;G) and (A;A) genotypes. A study of 200+ German patients indicated that (G;G) homozygotes were at 2x increased risk (CI: 1.32-2.92, p = 0.0007) for cluster headaches. A meta-analysis of 3 pooled studies concluded that the rs2653349(G;G) genotype showed a higher disease risk compared to the remaining genotypes (odds ratio 1.69, CI:1.11-2.5...
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rs3118470 increases susceptibility to Type I Diabetes 1.28 times for carriers of the C allele Impact of diabetes susceptibility loci on progression from pre-diabetes to diabetes in at-risk individuals of the diabetes prevention trial-type 1 (DPT-1). Joint genetic susceptibility to type 1 diabetes and autoimmune thyroiditis: from epidemiology to mechanisms. Follow-up analysis of genome-wide association data identifies novel loci for type 1 diabetes. Genetic association between the interleukin-2 receptor-alpha gene and mode of onset of type 1 diabetes in the Japanese population. Overview of the Rapid Response data. Analysis of 19 genes for association with type I diabetes in the Type I Diabetes Genetics Consortium families. [GWAS:Alopecia areata]
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related to Paget’s disease of bone 23andMe blog. [OMIM:?] [GWAS:Paget's disease]
1.6x risk for ICP
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rs3740066, a SNP in the ABCC2 gene, is reported to be associated with a higher risk of developing intrahepatic cholestasis of pregnancy (ICP) based on a study of ~70 Argentinian patients. ICP is associated with increased fetal risks such as premature birth or intrauterine death. The risk allele is rs3740066(A), and the odds ratio for homozygous rs3740066(A;A) mothers is 4.44 (CI: 1.83 - 10.78), and for heterozygous mothers 1.65 (CI: 0.76 - 3.64), compared to rs3740066(G;G) mothers. [PharmGKB:Curated The AUCs of irinotecan, SN-38, SN-38 glucuronide, and APC are influenced by rs3740066, rs2306283, rs35605, rs10276036, and rs717620 .]
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[GWAS:Telomere length]
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rs1800544 (C-1291G) is a SNP located in the promoter region of ADRA2A (adrenergic receptor alpha 2A). GG genotype carriers had significantly higher consumption of sweet food products (Estonian Children Personality Behavior and Health Study subset, n = 419) GG genotype carriers had significantly higher scores on an assessment of depression, and significantly lower scores on morality and orderliness compared to CC carriers. girls with CC and CG genotypes scored higher than boys with the same genotypes on an assessment of extraversion. boys with GG genotypes, however, scored higher than girls with GG genotypes. GG genotype assoc. w/ higher scores of inattention Food Preference [OMIM:ALPHA-2A-ADRENERGIC RECEPTOR; ADRA2A]
depends on [[rs1801252]]
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Also known as Arg389, variation at this SNP, located in the ADRB1 gene, may encode either the amino acid glycine or arginine at amino acid position 389 of the corresponding protein, the beta-1 adrenergic receptor (hence why it is frequently called Arg389Gly). This protein is the target of beta blocker drugs, and so how well the drug works to help lower a patients high blood pressure depends in part on this SNP. The status of this SNP is often reported together with the status of SNP rs1801252, which encodes an amino acid variant at position 49 of the same (ADRB1) protein. The rs1801253(G) allele encodes the glycine. One of the best known studies of the effects of these 2 separate SNPs on the average efficacy of the beta blocker metoprolol in lowering blood pressure (BP) can be summarized f...
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rs4570625 and rs4565946 linked to the pathogenesis of early-onset obsessive compulsive disorder Tourette's Syndrome
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The C allele of this SNP in the NR1H3 gene is associated with increased (but still low) risk of progressive supranuclear palsy. [PharmGKB:Non-Curated GWAS results: Genome-wide association analysis of metabolic traits in a birth cohort from a founder population. (Initial Sample Size: 4,763 individuals; Replication Sample Size: NR); (Region: 11p11.2; Reported Gene(s): NR1H3; Risk Allele: rs7120118-G); (p-value= 0.00000004).This variant is associated with HDL cholesterol.] [GWAS:HDL cholesterol]
Frequency: 46.0%
References:8
References:8
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Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. The role of obesity-associated loci identified in genome-wide association studies in the determination of pediatric BMI. Is the thrifty genotype hypothesis supported by evidence based on confirmed type 2 diabetes- and obesity-susceptibility variants? Common body mass index-associated variants confer risk of extreme obesity. Obesity genotype score and cardiovascular risk in women with type 2 diabetes mellitus. Novel obesity risk loci do not determine distribution of body fat depots: a whole-body MRI/MRS study. From monogenic to polygenic obesity: recent advances. Obesity and diabetes genes are associated with being born small for gestational age: results from the Auckland Birthweig...
4+ IQ points for breastfeeding
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4+ IQ points for breastfeeding with the AA or AG genotypes Breastfeeding and IQ [GWAS:Response to statin therapy]
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rs174575, has been investigated with respect to increased intelligence in breastfed children but not yielded any clear result. *Although there was no difference in IQ linked to the SNP alone, breastfed children carrying one or two copies of rs174575(C) had a significant (6 point) increase in IQ compared to carriers of the same allele who were not breastfed. For children who were homozygous non-carriers, i.e. rs174575(G;G) individuals, there was no effect of breastfeeding on IQ. *did not replicate those findings. In contrast to their study, (G;G) children exhibited the greatest difference between feeding methods such that breastfed children performed similarly irrespective of child genotype whereas formula fed (G;G) children performed worse than other children on formula milk Breastfeeding ...
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A study of 12,854 Japanese subjects replicated the finding of an association between rs7310409 and serum CRP levels. [PharmGKB:Curated GWAS Results: Loci Related to Metabolic-Syndrome Pathways Including LEPR, HNF1A, IL6R, and GCKR Associate with Plasma C-Reactive Protein: The Women's Genome Health Study (Initial Sample Size: 6,345 women; Replication Sample Size: NR; Risk Allele: rs7310409-A). This variant is associated with C-reactive protein levels.] [GWAS:None] [GWAS:C-reactive protein]
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Variant in the C13orf31 region associated with increased susceptibility to leprosy, according to the 23andMe blog 23andMe blog. The risk allele is G, and the odds ratio is 1.68. Other genes associated with both Crohn's disease and leprosy include NOD2 and TNFSF15, according to 23andMe's blog. Leprosy Susceptibility [PharmGKB:Non-Curated GWAS Results: Genome-wide assocation defines more than 30 distinct susceptibility loci for Crohn's disease (Initial Sample Size: 3,230 cases 4,829 controls; Replication Sample Size: 2,325 cases 1,809 controls 1,339 affected trios; Risk Allele: rs3764147-G).] [OMIM:?] [GWAS:Leprosy] [GWAS:Crohn's disease]
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Response to Interferon Beta Therapy
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rs3018362 increases susceptibility to Osteoporotic fractures for carriers of the A allele related to Paget’s disease of bone 23andMe blog. [OMIM:?] [GWAS:Paget's disease]
normal confers susceptibility for the development of sporadic CJD
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rs1799990, also known as Met129Val or M129V, is a SNP in the prion protein PRNP gene. The more common rs1799990(A) allele encodes the Met (methionine). Historically, since 1991 this SNP has been associated with risk for sporadic Creutzfeldt-Jakob disease, with homozygotes of both types apparently at increased risk compared to heterozygotes. More recently, this SNP has been related to long-term memory with (A;A) and (A;G) individuals recalling 17% more words than (G;G) individuals at 24h following learning. A further study of 12 individuals of each of the 3 possible genotypes showed that at both 30 minutes and 24 hour time lags, correlations between retrieval-related brain activity and retrieval success were negative for (G;) homozygotes (the more activity, the worse retrieval success), whi...
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Brain Aneurysm
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[GWAS:Orofacial clefts]
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Further noteworthy novel findings were observed between SNPs in ESR1 with testosterone levels (rs722208, mean difference = 8.8%, P = 7.37 x 10–6) and SRD5A2 with 3-androstanediol-glucuronide (rs2208532, mean difference = 11.8%, P = 1.82 x 10–6). Sex Hormone Regulation
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rs4410790 and rs2470893 influences habitual caffeine consumption [GWAS:None]
Normal otosclerosis risk
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Each C allele at rs3914132 decreases the likelihood of developing otosclerosis, which can cause hearing loss. [PharmGKB:Non-Curated In a GWAS done in Belgian-Dutch cases and controls (694 of each, split into a discovery and a replication set) and then in a second replication set of 455 French cases and 480 controls, rs3914132 was found to be associated with otosclerosis.] [OMIM:OTOSCLEROSIS; OTSC1] [GWAS:Otosclerosis]
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An association between freckling and rs2153271 [GWAS:Freckling]
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Variant in the RIPK2 gene associated with a reduced risk of leprosy in Asians, according to the 23andMe blog. The protective allele is A, and the odds ratio is 0.76. Leprosy Susceptibility [GWAS:Leprosy]
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rs2976392 and diffuse-type gastric cancer (allele-specific odds ratio (OR) = 1.62, 95% CI = 1.38-1.89, P = 1.11 x 10(-9)). Substitution of the C allele with the risk allele T at a SNP in the first exon (rs2294008, which has r(2) = 0.995, D' = 0.999 with rs2976392) reduces transcriptional activity of an upstream fragment of the gene [OMIM:PROSTATE STEM CELL ANTIGEN; PSCA] [GWAS:Bladder cancer]
1.52x increased myocardial infarction risk, 1.67x increased aneurysm risk
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A common variant on chromosome 9p21 affects the risk of myocardial infarction, and is further discussed in this blog post 23andMe blog aneurysm *rs700651 2 G 1.18x risk 1.56x risk *rs10958409 8 A 1.37x risk 1.79x risk *rs1333040 9 T 1.29x risk 1.67x risk Brain Aneurysm [PharmGKB:Non-Curated GWAS results: Susceptibility loci for intracranial aneurysm in European and Japanese populations. (Initial Sample Size: 1,580 European cases, 6,276 European controls; Replication Sample Size: 495 Japanese cases, 676 Japanese controls); (Region: 9q21.3; Reported Gene(s): CDKN2A, CDKN2B; Risk Allele: rs1333040-T); (p-value= 0.0000000001).This variant is associated with Intracranial aneurysm.] [OMIM:ANEURYSM, INTRACRANIAL BERRY, 6] [GWAS:Intracranial aneurysm]
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Gout (A) increased risk.
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related to Paget’s disease of bone 23andMe blog. [OMIM:?] [GWAS:Paget's disease]
References:9
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23andMe blog chronic lymphocytic leukemia *rs13397985 G 1.41 [PharmGKB:Non-Curated GWAS Results: A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia (Initial Sample Size: 505 cases, 1,438 controls; Replication Sample Size: 1,024 cases, 1,677 controls; Risk Allele: rs13397985-G). This variant is associated with Chronic lymphocytic leukemia.] [GWAS:None] [GWAS:Chronic lymphocytic leukemia]
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rs9287638 is located on chromosome 2q37 and lies downstream of the gene, HDAC4. HDAC4 is part of histone deactelyases enzyme class that deacteylates nucleosomal histones, thus acting as transcriptional correpresors. This SNP is associated with increased risk of androgenic alopecia (AGA). . Androgenic alopecia (male pattern baldness) affects up to 70% of men. Androgens especially dihydrotesterone (DHT) plays a key role in androgenic alopecia. With ageing, androgens reduces hair growth on the scalp and temples but leads to increased hair growth on the face. This phenomena is referred to as the androgen paradox Androgenic alopecia has an estimated heritability of 80% and is a polygenic trait. The strongest effect is seen with the X-chromosomal androgen receptor/ectodysplasin A2 receptor locus...
Frequency: 49.6%
References:0
References:0
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Persistant Fetal Hemoglobin Fetal Hemoglobin is produced in adulthood in people having at least one 'A' allele in Rs10195871
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Brain Aneurysm
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[OMIM:?] [GWAS:Alopecia areata]
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[GWAS:Obesity]
Frequency: 46.9%
References:1
References:1
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For photic sneeze reflex, we find a novel association with rs10427255 (score 10.9 and an OR of 1.32). We also find a suggestive association with rs11856995 (score 7.13 and OR of 0.78). The C allele appears to be associated with higher odds of photic sneezing. [GWAS:Common traits (Other)]
Frequency: 33.0%
References:5
References:5
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23andMe blog chronic lymphocytic leukemia *rs17483466 G 1.39 Genetic susceptibility for chronic lymphocytic leukemia among Chinese in Hong Kong. [PharmGKB:Non-Curated GWAS Results: A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia (Initial Sample Size: 505 cases, 1,438 controls; Replication Sample Size: 1,024 cases, 1,677 controls; Risk Allele: rs17483466-G). This variant is associated with Chronic lymphocytic leukemia.] [GWAS:None] [GWAS:Chronic lymphocytic leukemia]
Normal 0.97x risk for Age Related Macular Degeneration. When the retina cells in the eye get damaged with age, it is known as Age Related Macular Degeneration. This SNP has about the average risk. The SENS Research Foundation is working on a promising cure for Age Related Macular Degeneration: http://www.sens.org/outreach/conferences/lysosens-synthetic-biology-approach-treat-age-related-macular-degeneration
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may influence age related macular degeneration (damage to the eye with ageing) when part of the haplotype of rs1061170 rs3753394 rs800292 rs1329428 (TGTC), but does not appear to do so alone. age related macular degeneration [GWAS:Age-related macular degeneration]
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23andMe blog *Each G at rs2856683 increased the odds of primary biliary cirrhosis by 1.75x. *Each G at rs6441286 increased the odds of primary biliary cirrhosis by 1.54x. *Each A at rs3790567 increased the odds of primary biliary cirrhosis by 1.51x. Vaccine immunogenetics: bedside to bench to population. Replicated association of 17q12-21 with susceptibility of primary biliary cirrhosis in a Japanese cohort. A GWAS follow-up study reveals the association of the IL12RB2 gene with systemic sclerosis in Caucasian populations. Primary Biliary Cirrhosis: Preliminary Research [PharmGKB:Curated A GWAS of 2072 Canadian and U.S. subjects (536 patients with primary biliary cirrhosis and 1536 controls) showed that primary biliary cirrhosis was significantly and reproducibly associated with this SNP ...
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freckling [OMIM:OCA2 GENE]
Frequency: 34.5%
References:32
References:32
brown eye color
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rs12913832 is a SNP near the OCA2 gene that may be functionally linked to blue or brown eye color, due to a lowering of promoter activity of the OCA2 gene. Blue eye color is associated with the rs12913832(G;G) genotype. For green versus blue eye color rs12913832 in OCA2/HERC2 has a score of 51.5 and an estimated allelic OR of 8.43 . The SNP rs1667394 in this same region has an estimated OR of (4.85–10.06). rs12913832 is also part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, that is found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other racial groups. rs12913832-T (brown eye) homozygotes compared to rs12913832-C (blue eye). correlations with...
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rs1667394 increases susceptibility to Blond rather than brown hair 4.94 times for carriers of the A allele rs1667394 increases susceptibility to Blue rather than brown eyes 29.43 times for carriers of the A allele rs1667394 increases susceptibility to Blue rather than green eyes 6.74 times for carriers of the A allele For green versus blue eye color rs12913832 in OCA2/HERC2 has a score of 51.5 and an estimated allelic OR of 8.43 . The SNP rs1667394 in this same region has an estimated OR of (4.85–10.06). [OMIM:HECT DOMAIN AND RCC1-LIKE DOMAIN 2; HERC2] [GWAS:Eye color]
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23andMe blog chronic lymphocytic leukemia *rs7176508 A 1.37 [PharmGKB:Non-Curated GWAS Results: A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia (Initial Sample Size: 505 cases, 1,438 controls; Replication Sample Size: 1,024 cases, 1,677 controls; Risk Allele: rs7176508-A). This variant is associated with Chronic lymphocytic leukemia.] [GWAS:None] [GWAS:Chronic lymphocytic leukemia]
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association with obesity Obesity: Preliminary Research Measures of Obesity
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The T allele of rs9888739 is associated with higher risk of systemic lupus erythematosus. NEJM a combined analysis of the 7380 independent samples generated a maximum combined P=2.02x10–26 and an odds ratio of 1.65 for the association between the T allele of rs9888739 and lupus. [PharmGKB:Non-Curated GWAS Results: Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci (Initial Sample Size: 720 cases, 2,337 controls; Replication Sample Size: 1,846 cases, 1,825 controls; Risk Allele: rs9888739-T).] [GWAS:None] [GWAS:Systemic lupus erythematosus in women]
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Variant in the NOD2 gene associated with greater susceptibility to leprosy in Asians, according to the 23andMe blog. The risk allele is C, and the odds ratio is 1.59. Another gene associated with susceptibility to leprosy is TNFSF15. SNPs in both the NOD2 and TNFSF15 genes are also associated with susceptibility to Crohn's disease. Leprosy Susceptibility [GWAS:Leprosy]
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Adiponectin Levels
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Height
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Bladder Cancer Non-ABO Blood Groups [OMIM:?]
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This study compared 608 patients of European ancestry with papillary thyroid cancer, which is the most common form of thyroid cancer and is highly treatable, to 901 healthy controls. The authors found an association between the SNP rs2910164, which is equivalent to the 23andMe SNP rs2961920, and risk for thyroid cancer. People with the AC genotype at rs2961920 had about 1.5 times the odds of papillary thyroid cancer compared to those with the AA genotype and about three times the odds compared to the CC genotype. Though this is an atypical risk pattern, the researchers speculate in a separate paper that having one copy of each form of the SNP increases production of molecules that regulate the cell's response to DNA damage, a process that is often involved in cancer.
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news the presence of the G allele was protective against follicular lymphoma, while the presence of the A allele was predictive of an increased risk of developing follicular lymphoma. Dr. Brown said individuals who had the A variant were nearly twice as likely to develop follicular lymphoma. 23andMe blog coverage [OMIM:?] [GWAS:Follicular lymphoma]
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23andMe blog *Each G at rs2856683 increases the odds of primary biliary cirrhosis by 1.75x. *Each G at rs6441286 increased the odds of primary biliary cirrhosis by 1.54x. *Each A at rs3790567 increased the odds of primary biliary cirrhosis by 1.51x. Primary Biliary Cirrhosis: Preliminary Research [OMIM:?]
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[GWAS:Alopecia areata]
Frequency: 37.2%
References:0
References:0
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'Biological Aging' ('Telomere length') on 23andMe.
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower COMT enzymatic activity, therefore higher dopamine levels; lower pain threshold, enhanced vulnerability to stress, yet also more efficient at processing information under most conditions *rs4680(G) = Warrior. Val, less exploratory, higher COMT enzymatic activity, therefore lower dopamine levels; higher pain threshold, better stress resiliency, albeit with a modest reduction in executive cognition performance under most conditions Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis; summary at ) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compar...
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[PharmGKB:Curated On the basis of subjects' pain responsiveness, haplotypes involving rs6269 (A/G), rs4633 (C/T), rs4818 (C/G), and rs4680 (G/A) were designated as low (low pain sensitivity (LPS) haplotype; GCGG), average (average pain sensitivity (APS) haplotype; ATCA), or high (high pain sensitivity (HPS) haplotype; ACCG) pain sensitive.]
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'''rs2269726''' is located in intron 5 within the GNB1L gene on chromosome 22q11. In males, the homozygous genotype, irrespective of whether it is the ancestral (C) or derived (T) allele, is associated with higher risk for schizophrenia than the heterozygous. A 2008 paper showed the association (P = 1.8 × 10-5 (significant in this study); OR = 1.46) in a candidate gene study using a combined German-British sample of 1,408 cases and 2,746 controls. Previous evidence linking GNB1L to schizophrenia includes higher incidence of schizophrenia among those with 22q11 deletions and genetic linkage studies. A well-documented ~3 Mb deletion on chromosome 22q11 is characteristic among those with a variety of psychiatric disorders—together termed 22q11 deletion syndrome (22q11DS)—incl...
normal
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rs662799 is a SNP in the APOA5 gene. The rarer rs662799(C) allele has been associated in multiple reports (cited below) to be associated with higher triglyceride levels. Independently of triglyceride levels, perhaps, a study based on 1,864 Italian patients <45 years old at the time of their first heart attack (myocardial infarction) concluded that this SNP is associated with higher risk for an early heart attack, with a per C allele odds ratio of 1.44 (CI: 1.23-1.69, p = 6.7 × 10(-5)). This SNP has also been reported to help prevent weight gain from high fat diets. 1,073 men and 1,207 women participating in the Framingham Offspring Study rs662799 -1131T>C in modulates the effect of fat intake on BMI and obesity risk in both men and women. Individuals with at least one C allele g...
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[PharmGKB:Non-Curated GWAS Results: Two newly identified genetic determinants of pigmentation in Europeans (Initial Sample Size: 5,130 individuals; Replication Sample Size: 3,330 individuals; Risk/trait Allele: rs1408799-C). This variant is associated with Blue vs. green eyes.] [OMIM:TYROSINASE-RELATED PROTEIN 1; TYRP1] [GWAS:Eye color] [GWAS:Blue vs. green eyes]
normal
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rs1447295 is a SNP on chromosome 8q24, associated with increased risk for prostate cancer in several studies. In a study of over 3,600 Caucasians with prostate cancer, rs1447295 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On their own, the rs1447295(A;A) and (A;C) risk genotypes yield an odds ratio for developing prostate cancer of 1.22 (CI: 1.06-1.40, p=5.3x10-3) and may account for 5.4% of population attributable risk. The rs1447295] location could be responsible for about seven percent of prostate cancer cases in white men of north European descent. Thus, taken together with rs6983267, these two genetic changes could account for as much as one quarter of prostate cancer cases in white men. The increased risk was observed for all...
normal
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This is basically a surrogate for rs7442295, and thus associated with higher serum urate levels. [OMIM:SOLUTE CARRIER FAMILY 2 (FACILITATED GLUCOSE TRANSPORTER), MEMBER] [GWAS:Uric acid levels]
common in complete genomics
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rs4140564, a SNP on chromosome 1 near the PTGS2 and PLA2G4A genes, has been associated with knee osteoarthritis. A study of 255 British patients, replicated subsequently in ~2,000 UK, Dutch and US patients, found that rs4140564 was associated with knee osteoarthritis in all populations studied with an overall odds ratio = 1.55, CI: 1.30-1.85, p < 6.9 x 10e-7. [PharmGKB:Curated GWAS results: Genome-wide Association Scan Identifies a Prostaglandin-Endoperoxide Synthase 2 Variant Involved in Risk of Knee Osteoarthritis (Initial Sample Size: 357 cases, 285 controls; Replication Sample Size: 1,177 cases, 2,372 controls). This variant is associated with Knee osteoarthritis.] [GWAS:Knee osteoarthritis]
normal/common
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rs6025 represents a SNP in the Factor V F5 gene, encoding a change in the protein from an arginine at position 506 to a glutamine. The resulting rs6025(A) allele encodes a mutation known as the Leiden mutation, R506Q, found in perhaps 3 to 5% of the individuals in most populations. About 1 in 10 individuals harboring the R506Q will experience clinically significant venous thromboembolism in their lifetimes (according to OMIM). Overall, the rs6025(A) allele appears to be necessary but not sufficient for the development of venous thromboembolism. Patients who are rs6025(A;G) heterozygotes but lack other risk-enhancing SNPs have a risk of recurrent deep venous thrombosis equal to patients with no such SNPs. In contrast, patients who are heterozygotes for both rs6025 and the prothrombin rs1799...
common
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rs7566605 was initially reported as being associated in at least 4 independent populations as being associated with obesity however replications are inconsistent, and a recent (2009) large meta-analysis comprising 34 studies (and over 70,000 subjects) has concluded that there is no evidence for overall association of the rs7566605 polymorphism with obesity. See also: Poster At least one population has since been reported in which this association was not seen. Furthermore, a study of 18,000 Danish subjects also failed to find any direct role for this SNP in the development of obesity, except that among physically inactive subjects, (C)-allele carriers tended to have a higher body mass index (by O.5 kg/m2) than (G)-allele carriers. On the other hand, a report has also been published indicat...
Normal risk for autoimmune disorders
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This SNP, located in the PTPN22 gene and also known as R620W, or 1858C>T, may influence Rheumatoid Arthritis and other autoimmune diseases, including but not limited to, multiple sclerosis, Crohn's disease, celiac disease and type-1 diabetes. In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for type-1 diabetes for this SNP was recalculated to be 1.98 (CI 1.82-2.15). rs2476601 was confirmed in another 2007 study to be a risk factor for RA . * confirms the association of rs2476601 rheumatoid arthritis * two copies of the PTPN22 R620W allele more than doubles the risk for RF positive RA * see rs2476601(A;G) * * * * * rs2476601 shows a 0.75 (r squared) correlation with rs6679677, a SNP in the RSBN1 gene associated with rheumatoid arthritis...
normal risk
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The more common allele of rs761100 has been linked to increased risk for developmental dyslexia in a study of ~300 British families. While odds ratios were not reported, the significance was reported as p=0.02. Convergent genetic linkage and associations to language, speech and reading measures in families of probands with Specific Language Impairment. Developmental Dyslexia
1 genoset 106 snps
(hide) African American
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In 'Association of the ADRA2A polymorphisms with the risk of type 2 diabetes: a meta-analysis.' a meta-analysis of publications prior to September 2012 showed no overall association between rs553668 and T2D risk, but did find an association with very high (poor) P-value for Europeans under recessive gene model (GT=AA, OR=1.36, p=0.02, 95% CI: 1.05, 1.76). In 'Genetic association of adrenergic receptor alpha 2A with obesity and type 2 diabetes.' rs553668 was found to correlate with obesity in Swedish population, but not significantly for BMI-corrected T2D risk. ADRA2A is involved in sympathetic nervous system's inhibition of insulin secretion and lipolysis, so direct effect on T2D is usually sought, but the Swedish study suggest it could work through body mass. It also mentions that rs55366...
1 snp
(hide) Ageing
watch out for high fat in diet
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rs1801282, also known as Pro12Ala, is a common SNP in the peroxisome proliferator-activated receptor PPARG gene. The more common (C) allele (in dbSNP orientation) encodes the 'Pro' amino acid at this SNP position. rs1801282 has been reported to be associated with metabolic syndrome, but other studies have not been able to replicate any strong or significant effect. The association between type-2 diabetes and SNP rs1801282 is mentioned as being replicated in rs1801282 and risk of cognitive decline in elders? Maybe with diabetes. A ten-year study of 679 male patients with symptomatic coronary artery disease found that rs1801282(G) carriers had a much lower (10 year) cardiovascular risk, with the hazard ratio estimated to be 0.10 (CI: 0.01-0.70, p = 0.02) for ischemic heart disease and 0.24 f...
Avg. fasting Plasma Glucose 5.18 mmol/L (93 mg/dl). Slightly higher blood glucose. Fasting Plasma Glucose is the amount of sugar in your blood when you wake up. It's required to power your body, but too much is very bad for you. Fasting plasma glucose between 5.6 mmol/L and 6.9 mmol/L (101 – 125 mg/dl) is considered pre-diabetes. Fasting plasma glucose higher than 7 mmol/L (126 mg/dl) is considered diabetes.
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rs560887, p = 4 x 10(-7)) *654 normoglycemic subjects, replicated in 9,353 subjects *fasting plasma glucose (FPG) (beta = -0.06 mmol/l per A-allele, combined p = 4 x 10(-23)) and with pancreatic beta-cell function (Homa-B model, combined p = 3 x 10(-13)) in three populations; however it was not associated with type 2 diabetes risk. (ageing) Blood Glucose [PharmGKB:Non-Curated Phenotype 1: In a meta-analysis of 21 GWAS cohorts followed by analysis in additional individuals, this SNP was found to be associated with fasting glucose level. Study size: 119,169. Significance metric(s): p = 8.7 x 10(-218). Phenotype 2: In the same study, this SNP was found to be associated with HOMA-B (homeostasis model assessment of beta-cell function). Study size: 94,839. Significance metric(s): p = 1.5 x 10(-...
Low IGF-1 level, linked to number of diseases rs2229765(A;A) associated with ischemic stroke (OR = 1.641, P = 0.022) in a Chinese population After adjustment for smoking, alcohol drinking, history of hypertension, and body mass index, IGF-1R AA genotype was still significantly associated with an increased risk of IS (OR = 1.787, P = 0.029), compared with IGF-1R GG. The frequency of A-allele in advanced CRC was significantly higher then early CRC (52 vs. 37.7, OR = 1.78). According to genotype serum IGF-1 levels was significantly decreased in patients with GG genotype then patients with dominant genotypes. Our results showed a relationship between the +3179G>A polymorphism of the IGF-1R and serum IGF-1 with the progression of colorectal carcinoma.
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rs2229765(A;A) associated with ischemic stroke (OR = 1.641, P = 0.022) in a Chinese population
Normal (worse) aging. This is the less beneficial version of the SIRT1 longevity gene, which doesn't extend lifespan. It is normal in non-Asians. It has more cognitive decline with age. Taking resveratrol is also believed to increase longevity via the SIRT1 gene, so it might (or might not) be possible to mitigate this with resveratrol supplements or some other SIRT1 activator.
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rs3758391, a SNP in the SIRT1 gene, has been reported to potentially have some role in either longevity, or with higher statistical significance, better cognitive function in older individuals. SIRT1 is thought to regulate neuronal metabolism and survival in response to stress, and the equivalent gene in other species influences maximal life span. The study reporting improved cognition for carriers of rs3758391(T) alleles was based on over 1,000 Finnish adults over the age of 85, and a weak trend towards lower cardiovascular disease was also reported for this allele.
Lower risk of dementia and Alzheimer's disease. Higher good cholesterol. One copy of a longevity gene. This seems to raise HDL ('good') cholesterol, and reduce the risk of dementia and Alzheimer's disease. It may slightly increase longevity. It has been particularly studied in Ashkenazi Jews.
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This SNP rs5882 in the CETP gene referred to as ILE405VAL and RSAI405V has been related to ageing and exceptional long life. A study in Ashkenazi Jews showed that individuals homozygotic for the G allele have significantly longer lifespans. New research also indicates that G homozygotes have an average of 70% less risk of dementia and Alzheimer's disease. The study also found that heterozygotes have a lower risk of dementia and Alzheimer's disease but more study is needed to determine the risk reduction for heterozygotes. See Association of a Functional Polymorphism in the Cholesteryl Ester Transfer Protein (CETP) Gene With Memory Decline and Incidence of Dementia and CETP Variant Linked to Slower Cognitive Decline and Reduced Dementia Risk . [PharmGKB:Curated Risk or phenotype-associated...
Common variant. Slightly shorter lifespan. Chemotherapy is less effective. Accelerated lung decline in smokers. African Americans have 2.15x risk of dying from colo-rectal cancer.
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This SNP, a variant in the TP53 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the G allele encodes an arginine at position 72 of the protein (where there's normally a proline), and the SNP is commonly called the Arg72 variant, although P72R and Arg72Pro are also common in the literature. Minor allele homozygotes, i.e. rs1042522(C;C) genotypes, live on average 3 years longer than major allele (G;G) homozygotes, based on a study of 9,200+ Danish individuals. The increased longevity is speculated to be related to the i...
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[GWAS:Telomere length]
Frequency: 51.3%
References:1
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Synergistic association of mitochondrial uncoupling protein (UCP) genes with schizophrenia. A genetic association analysis of cognitive ability and cognitive ageing using 325 markers for 109 genes associated with oxidative stress or cognition. Ala55Val polymorphism on UCP2 gene predicts greater weight loss in morbidly obese patients undergoing gastric banding. Lack of association between uncoupling protein-2 Ala55Val polymorphism and incident diabetes in the atherosclerosis risk in communities study. Ser1369Ala variant in sulfonylurea receptor gene ABCC8 is associated with antidiabetic efficacy of gliclazide in Chinese type 2 diabetic patients. Human uncoupling protein 2 and 3 genes are associated with obesity in Japanese. Physiogenomic comparison of edema and BMI in patients receiving ros...
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Data-mining analysis suggests an epigenetic pathogenesis for type 2 diabetes. Genetic prediction of future type 2 diabetes. Interaction between the UCP2-866G/A, mtDNA 10398G/A and PGC1alpha p.Thr394Thr and p.Gly482Ser polymorphisms in type 2 diabetes susceptibility in North Indian population. Association between obesity and insulin resistance with UCP2-UCP3 gene variants in Spanish children and adolescents. Association of genetic variants with chronic kidney disease in Japanese individuals. Polymorphisms of the UCP2 gene are associated with proliferative diabetic retinopathy in patients with diabetes mellitus. Interaction between the UCP2 -866 G>A polymorphism, diabetes, and beta-blocker use among patients with acute coronary syndromes. Effect of the common -866G/A polymorphism of the u...
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rs1367117 (C711T/711C>T) is a SNP within APOB (Apolipoprotein B). among 97 hypertensive subjects, C allele carriers responded to irbesartan with an average blood pressure reduction of 19 mmHg, however, they did not respond to atenolol associated with apoB levels [PharmGKB:Curated The APOB:711C>T, C allele was associated with reduction of blood pressure in response to irbesartan treatment but not atenolol treatment.] [OMIM:?] [GWAS:None]
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Multiple genetic determinants of plasma lipid levels in Caribbean Hispanics. beta-Carotene conversion products and their effects on adipose tissue.
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[GWAS:None]
higher blood pressure if <50
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rs8192678 encodes a SNP also known as Gly482Ser; the (A) allele encodes the Ser. Some reports have linked this SNP to risk for hypertension and systolic blood pressure (SBP). However, a meta-analysis of 13,000+ individuals did not find any such association. However, gene-age interaction was apparent. For diastolic blood pressure (DBP), p(interaction)<0.0001; for systolic BP, p(interaction)=0.026. In younger individuals (<50yrs; n=2511) the rs8192678(A) allele was associated with higher DBP (p=4.2 x 10<sup>-12</sup>) and SBP (p=7.2 x 10<sup>-12</sup>), but no association was evident for individuals over 50yrs (n=5088). Analysis of PGC-1alpha variants Gly482Ser and Thr612Met concerning their PPARgamma2-coactivation function. PPARGC1A coding variation may initiat...
References:1
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Associated with risk of lung cancer in a Chinese population Effects of the type 2 diabetes-associated PPARG P12A polymorphism on progression to diabetes and response to troglitazone.
elevated lipids
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rs693 increases susceptibility to Elevated Apolipoprotein B and LDL-Cholesterol for carriers of the T allele [PharmGKB:Non-Curated GWAS results: Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. (Initial Sample Size: 17,797 individuals; Replication Sample Size: NR); (Region: 2p24.1; Reported Gene(s): APOB; Risk Allele: rs693-G); (p-value= 0.00000000000000004).This variant is associated with LDL cholesterol.] [OMIM:APOLIPOPROTEIN B; APOB] [GWAS:Cholesterol, total]
Normal 0.97x risk for Age Related Macular Degeneration. When the retina cells in the eye get damaged with age, it is known as Age Related Macular Degeneration. This SNP has about the average risk. The SENS Research Foundation is working on a promising cure for Age Related Macular Degeneration: http://www.sens.org/outreach/conferences/lysosens-synthetic-biology-approach-treat-age-related-macular-degeneration
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may influence age related macular degeneration (damage to the eye with ageing) when part of the haplotype of rs1061170 rs3753394 rs800292 rs1329428 (TGTC), but does not appear to do so alone. age related macular degeneration [GWAS:Age-related macular degeneration]
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[GWAS:None]
38 snps
(hide) Anger
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[GWAS:Anger]
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[GWAS:Anger]
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[GWAS:Anger]
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[GWAS:Anger]
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[GWAS:Anger]
6 snps
(hide) APOE
Possibly lower levels of ApoE
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Significant Alzheimer's disease associations with were found for rs449647(A;A) and rs405509(G;G) genotypes (positive), and rs449647(A;T) and rs405509(T;T)
normal
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Conflicting reports of possible small increase in Alzheimer's risk. Currently dubious at best. rs2373115 is one of several SNPs in the GAB2 gene indicating an increased risk (OR 4.1) of late-onset Alzheimer's disease, but apparently only in individuals also carrying ApoE4 alleles, i.e. rs429358(C) alleles rs2373115 marker does not modify the risk of Alzheimer's disease in Spanish APOE e4 carriers. rs2373115(G) is the risk allele. (p = 9 x 10(-11)) was associated with an odds ratio of 4.06 (confidence interval 2.81-14.69) However, a separate study of 1,749 Alzheimer patients concluded that this GAB2 SNP is 'at best a minor genetic determinant' since the authors of this study observed only a slight tendency for an increase of the (G;G) genotype (odds ratio of 1.3 vs (G;T) and (T;T), CI:1.0-1...
more likely to gain weight if taking olanzapine
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rs5092 is a SNP in the apolipoprotein A4 APOA4 gene. In a study of 67 mostly Caucasian patients prescribed the atypical antipsychotic olanzapine, carriers of a rs5092(G) allele were less likely to gain significant weight compared to rs5092(A;A) carriers, as assessed by physiogenomic analysis of corresponding weight profiles. Two other SNPs, rs4765623 and rs7412, were also significantly associated with weight profiles in these patients.
more likely to gain weight if taking olanzapine
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rs4765623 is a SNP in the scavenger receptor class B, member 1 SCARB1 gene. In a study of 67 mostly Caucasian patients prescribed the atypical antipsychotic olanzapine, carriers of a rs4765623(C) allele were more likely to gain significant weight compared to rs4765623(T;T) carriers, as assessed by physiogenomic analysis of corresponding weight profiles. Two other SNPs, rs5092 and rs7412, were also significantly associated with weight profiles in these patients. Combining fMRI and SNP data to investigate connections between brain function and genetics using parallel ICA. [GWAS:None]
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obstructive sleep apnea rs405509 Significant Alzheimer's disease associations with were found for rs449647(A;A) and rs405509(G;G) genotypes (positive), and rs449647(A;T) and rs405509(T;T) [PharmGKB:Curated A study in 2150 Japanese individuals with metabolic syndrome, including 411 subjects with chronic kidney disease (CKD) and 1739 controls found that the -219G-->T SNP in APOE (rs405509) was most significantly associated with CKD in Japanese individuals with metabolic syndrome.]
increased risk in men for biliary conditions
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rs440446 is a SNP in an intron of the apolipoprotein E APOE gene; it is also known as the IVS1+69 variant. In a study of ~1,000 Chinese patients with various biliary tract conditions, including cancer and gallstones, men carrying a rs440446(C) allele (in dbSNP orientation) had a 1.7x risk of gallstone disease [CI: 1.2-2.4], a 1.8x risk of gallbladder cancer (CI: 1.0-3.3), a 3.7x risk of bile duct cancer (CI: 2.0-7.0), and a 4x risk of ampullary cancer (CI: 1.4-12.4). Note: orientation relative to dbSNP entry is reversed as published. Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity and osteoporosis. Patterns of linkage disequilibrium and haplotype distribution in disease candidate genes. Subarachnoid hemorrh...
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This appears to be the snp on the Illumina Human 550 which is closest to rs4420638 [PharmGKB:Non-Curated GWAS results: Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. (Initial Sample Size: 17,815 individuals; Replication Sample Size: NR); (Region: 19q13.32; Reported Gene(s): TOMM40, APOE; Risk Allele: rs439401-G); (p-value= 0.000000002).This variant is associated with Triglycerides.] [GWAS:Triglycerides]
normal
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rs5963409 is a SNP in the ornithine carbamoyltransferase OTC gene; this SNP is also known as the -389 G/A SNP. Previous association studies were extended to a population of 2113 Alzheimer's disease cases and 1580 controls from northern France, western France, the United Kingdom and Italy. The rs5963409(A) minor allele was weakly but significantly associated with an increased risk of developing Alzheimer's disease (odds ratio 1.19, p = 0.004). This association was independent of age and ApoE status.
normal risk
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rs1050283, a SNP also known as +1073, is located in the 3' untranslated region of the oxidized low density lipoprotein (lectin-like) receptor 1 OLR1 gene, which is also known as the LOX-1 gene. The rs1050283(C) allele has been associated with increased risk for Alzheimer's disease in several studies of ~200 Southern Italian Alzheimer patients. The risk is independent of ApoE status, and may also be defined by haplotypes including one or both of neighboring SNPs rs12316150 and rs669.
normal risk for Alzheimer's; higher total and LDL cholesterol in females
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RNA made containing the rs688(T) SNP, a variant near exon 12 of the low-density lipoprotein receptor (LDLR) that is a receptor for ApoE proteins, is spliced at lower efficiency in males. Presumably due to this, the rs688(T;T) genotype was associated with increased risk for Alzheimer's disease odds in males (odds ratio 1.49, CI: 1.13-1.97, uncorrected p=0.005), but not in females. The presence of the rs688(T) allele associates with increased total and LDL-cholesterol in female members of the Framingham Offspring Study; rs688 was not associated with significant differences in HDL-cholesterol. The largest rs688-associated cholesterol differences were observed in pre-menopausal women. Taken together, rs688, a SNP present in approximately 60% of Caucasians, is associated with significant 10% in...
10 snps
(hide) Appearance
0.61x reduced risk of Male Pattern Baldness. Discovered by 23andWe based on customer surveys, and considered preliminary research.
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This is the 23andWe discovery: 'Male Pattern Baldness: Preliminary Research'. It affects appearance.
1.68x increased risk of cleft lip
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risk of cleft lip 23andMe considers rs861020 a proxy Associated with European Facial Appearance *rs7590268 *rs16903544 *rs987525 *rs9574565 *rs227731 *rs642961 *rs1258763 Genome scan, fine-mapping, and candidate gene analysis of non-syndromic cleft lip with or without cleft palate reveals phenotype-specific differences in linkage and association results. Lack of association between IRF6 polymorphisms (rs2235371 and rs642961) and non-syndromic cleft lip and/or palate in a Brazilian population. Current concepts in genetics of nonsyndromic clefts. Studies of palatine rugae and interferon regulatory factor 6 variations in a group of families with sporadic hypodontia. IRF6 gene variants in Central European patients with non-syndromic cleft lip with or without cleft palate. Family-based study sh...
Generally European; Light skin; Possibly an increased risk of melanoma This SNP is associated with skin, hair, and eye colour, and risk of melanoma. Individuals with the G;G genotype are generally of European descent and have fair skin. In a population-based case-control study investigating a number of pigmentation-related SNPs and their correlation with cutaneous malignant melanoma (CMM) in a Caucasian Australian population, rs16891982 (variant F374L) was found to be associated with odds ratios of 3.44, 2.86, 1.68, and 1.68 for all study subjects (1,738 CMM cases and 4,517 controls); subjects with northern European ancestry (1,438 cases and 3,098 controls); northern European subjects adjusted for hair, eye, and skin colour; and northern European subjects adjusted for the MC1R genotype, r...
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This snp influences skin pigmentation. The allele p.L374F indicates light-skinned european ancestry c.1122C>G, p.Phe374Leu (NCBI dbSNP rs16891982) in SLC45A2 was associated with protection from malignant melanoma (OR, 0.41; 95% CI, 0.24-0.70; P=0.008 after adjustment for multiple testing) An association study conducted on a population of European origin concluded that the rare (in Europeans, at least) allele L374, i.e. rs16891982(C) in dbSNP orientation, significantly increases the possibility of having black hair color, with an odds ratio of around 7. This population-based case-control study investigated a number of pigmentation-related SNPs and their correlation with cutaneous malignant melanoma (CMM) in an Australian population. rs16891982 (variant F374L) was found to be associated w...
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[PharmGKB:Non-Curated GWAS Results: Two newly identified genetic determinants of pigmentation in Europeans (Initial Sample Size: 5,130 individuals; Replication Sample Size: 3,330 individuals; Risk/trait Allele: rs35264875-T). This variant is associated with Blond vs. brown hair.] [OMIM:TWO-PORE SEGMENT CHANNEL 2; TPCN2] [GWAS:Blond vs. brown hair]
None
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Influences appearance The A allele of rs1042602 is associated with the absence of freckles [PharmGKB:Non-Curated GWAS Results: A genomewide association study of skin pigmentation in a South Asian population (Initial Sample Size: 363 with maxL* < 56 and 374 with maxL* > 63; 20% tails of distribution; Replication Sample Size: 116 low maxL*, 115 high maxL* individuals). This variant is associated with skin pigmentation by reflectance spectroscopy.] [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 3; SHEP3] [GWAS:Freckles] [GWAS:Skin pigmentation by reflectance spectroscopy]
Frequency: 47.8%
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Influences appearance gnxp
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Associated with European Facial Appearance *rs7590268 *rs16903544 *rs987525 *rs9574565 *rs227731 *rs642961 *rs1258763 [GWAS:Nonsyndromic cleft lip with or without cleft palate]
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Influences appearance gnxp [OMIM:AGOUTI SIGNALING PROTEIN; ASIP]
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Associated with European Facial Appearance *rs7590268 *rs16903544 *rs987525 *rs9574565 *rs227731 *rs642961 *rs1258763 [GWAS:Nonsyndromic cleft lip with or without cleft palate]
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Influences appearance gnxp A genomewide association study of skin pigmentation in a South Asian population. Complex signatures of selection for the melanogenic loci TYR, TYRP1 and DCT in humans.
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blog The two most significant associations found were between nose width and SNP rs1258763 near the GREM1 gene in the German cohort (P=6 × 10?4), and between bizygomatic distance and SNP rs987525 at 8q24.21 near the CCDC26 gene (P=0.017) Genetic determination of human facial morphology: links between cleft-lips and normal variation. Associated with European Facial Appearance *rs7590268 *rs16903544 *rs987525 *rs9574565 *rs227731 *rs642961 *rs1258763 [GWAS:Nonsyndromic cleft lip with or without cleft palate]
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Associated with European Facial Appearance *rs7590268 *rs16903544 *rs987525 *rs9574565 *rs227731 *rs642961 *rs1258763 [GWAS:Nonsyndromic cleft lip with or without cleft palate]
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plos the association between rs12203592 and hair color was independent of rs1540771, a SNP between the IRF4 and EXOC2 genes previously found to be associated with hair color. [PharmGKB:Non-Curated GWAS Results: Genetic determinants of hair, eye and skin pigmentation in Europeans (Initial Sample Size: 2,986 individuals; Replication Sample Size: 3,932 individuals). This variant is associated with freckles.] [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 8; SHEP8] [GWAS:Freckles]
normal
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rs4911414 is a SNP near the ASIP (agouti signaling protein) gene on chromosome 20. This SNP is one of a tightly-linked pair that increases the likelihood of an individual being prone to sun sensitivity, in other words, freckles and sunburn, based on a study of 6,000+ Caucasians (5,000+ Icelanders + 1,000+ Dutch). The odds ratios, presumably on a dominant basis, and at least in the largest population (Icelanders) for 'freckles and burns vs. no freckles and tans' for the haplotype pair rs1015362(G) - rs4911414(T) is 3.91 (CI: 2.54-6.03) for males and 2.42 (CI: 1.52-3.86) for females, with an overall p=0.051. Based on a study by the same authors of 4,000+ skin cancer patients, this haplotype was seen to confer significant increased risk for cutaneous malignant melanoma (odds ratio 1.45, p = 1...
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Influences appearance gnxp Digital Quantification of Human Eye Color Highlights Genetic Association of Three New Loci[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865509/] Common sequence variants on 20q11.22 confer melanoma susceptibility. Genome-wide association study identifies three loci associated with melanoma risk. Web-based, participant-driven studies yield novel genetic associations for common traits.
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[PharmGKB:Non-Curated GWAS Results: Two newly identified genetic determinants of pigmentation in Europeans (Initial Sample Size: 5,130 individuals; Replication Sample Size: 3,330 individuals; Risk/trait Allele: rs1408799-C). This variant is associated with Blue vs. green eyes.] [OMIM:TYROSINASE-RELATED PROTEIN 1; TYRP1] [GWAS:Eye color] [GWAS:Blue vs. green eyes]
17 snps
(hide) Appearance/Eye color
Frequency: 47.8%
References:0
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Influences appearance gnxp
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Influences appearance gnxp [OMIM:AGOUTI SIGNALING PROTEIN; ASIP]
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Influences appearance gnxp A genomewide association study of skin pigmentation in a South Asian population. Complex signatures of selection for the melanogenic loci TYR, TYRP1 and DCT in humans.
normal
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rs4911414 is a SNP near the ASIP (agouti signaling protein) gene on chromosome 20. This SNP is one of a tightly-linked pair that increases the likelihood of an individual being prone to sun sensitivity, in other words, freckles and sunburn, based on a study of 6,000+ Caucasians (5,000+ Icelanders + 1,000+ Dutch). The odds ratios, presumably on a dominant basis, and at least in the largest population (Icelanders) for 'freckles and burns vs. no freckles and tans' for the haplotype pair rs1015362(G) - rs4911414(T) is 3.91 (CI: 2.54-6.03) for males and 2.42 (CI: 1.52-3.86) for females, with an overall p=0.051. Based on a study by the same authors of 4,000+ skin cancer patients, this haplotype was seen to confer significant increased risk for cutaneous malignant melanoma (odds ratio 1.45, p = 1...
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Influences appearance gnxp Digital Quantification of Human Eye Color Highlights Genetic Association of Three New Loci[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865509/] Common sequence variants on 20q11.22 confer melanoma susceptibility. Genome-wide association study identifies three loci associated with melanoma risk. Web-based, participant-driven studies yield novel genetic associations for common traits.
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[PharmGKB:Non-Curated GWAS Results: Two newly identified genetic determinants of pigmentation in Europeans (Initial Sample Size: 5,130 individuals; Replication Sample Size: 3,330 individuals; Risk/trait Allele: rs1408799-C). This variant is associated with Blue vs. green eyes.] [OMIM:TYROSINASE-RELATED PROTEIN 1; TYRP1] [GWAS:Eye color] [GWAS:Blue vs. green eyes]
6 snps
(hide) Ashkenazi Jews
1.3x increased risk for type-2 diabetes
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The accuracy of claims about this snp are called into question by table 1 of discusses the process of including this snp into Coriell and raises some doubt about the value of its inclusion. rs7754840 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.28 (CI: 1.17-1.41, p = 4.5 x 10e-7) type-2 diabetes Carriers of the (C;G) and (C;C) genotypes of rs7754840 had 11% and 24% lower first-phase insulin release in an IVGTT compared to that in carriers of the (G;G) genotype (P=0.002). The C allele was also associated with higher glucose area under the curve in an OGTT (P=0.016). rs7754840 type-2 diabetes Ashkenazi Jewish population shows an even stronger effect for rs7754840 than the general Caucasian population, based on 1,131 cases versus 1,147 co...
1.20x risk for breast cancer
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Based on a study of ~2500 female patients of European ancestry with sporadic postmenopausal breast cancer, this SNP in the FGFR2 showed the greatest risk. The risk allele is rs1219648(G), with a pooled odds ratio of 1.64 (CI:1.42-1.90) for rs1219648(G;G) homozygotes, and an odds ratio of 1.20 (CI: 1.07-1.42) for rs1219648(A;G) heterozygotes, compared with rs1219648(A;A) homozygotes. rs1219648 represents the SNP in the FGFR2 gene with the strongest association with breast cancer. However, nearby SNPs are almost as predictive. In particular, the following SNP alleles all have linkage values of 0.96 or greater with the rs1219648(G) allele in European populations: *rs2981579(A) *rs2420946(T) *rs11200014(A) An experimental rationale is presented indicating that this SNP is part of a haplotype t...
Lower risk of dementia and Alzheimer's disease. Higher good cholesterol. One copy of a longevity gene. This seems to raise HDL ('good') cholesterol, and reduce the risk of dementia and Alzheimer's disease. It may slightly increase longevity. It has been particularly studied in Ashkenazi Jews.
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This SNP rs5882 in the CETP gene referred to as ILE405VAL and RSAI405V has been related to ageing and exceptional long life. A study in Ashkenazi Jews showed that individuals homozygotic for the G allele have significantly longer lifespans. New research also indicates that G homozygotes have an average of 70% less risk of dementia and Alzheimer's disease. The study also found that heterozygotes have a lower risk of dementia and Alzheimer's disease but more study is needed to determine the risk reduction for heterozygotes. See Association of a Functional Polymorphism in the Cholesteryl Ester Transfer Protein (CETP) Gene With Memory Decline and Incidence of Dementia and CETP Variant Linked to Slower Cognitive Decline and Reduced Dementia Risk . [PharmGKB:Curated Risk or phenotype-associated...
Frequency: 38.1%
References:3
References:3
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rs11098403 is an intergenic SNP on chromosome 4 located ~300kb upstream of the 5' end of the NDST3 gene. Although in one publication the rs11098403(G) allele is said to be associated with increased risk for schizophrenia (odds ratio of 1.4, at least in Ashkenazi Jews), in another report this same allele is associated with decreased risk (odds ratio 0.6, in Han Chinese).,
4 snps
(hide) BCHE
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This SNP, on chromosome 3 upstream of BCHE (butyrylcholinesterase), is associated with higher cerebral amyloid deposition. The risk allele is G. [http://www.nature.com/mp/journal/vaop/ncurrent/fig_tab/mp201319f4.html]
possible increased Alzheimer's risk
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The rs1803274(A) allele encodes a version of the butyrylcholinesterase enzyme known as the K variant; it may also be known as CHE*539T or BCHE*539T. The allele produces a 30% reduction in serum butyrylcholinesterase activity, and it is often co-inherited with the SNP encoding the so-called 'atypical' butyrylcholinesterase, rs1799807. Although not replicated by other studies, some studies have found, at least in certain populations, a possible association between this SNP and risk for Alzheimer's disease (independent of ApoE4 status): * reports ~2x increased Alzheimer's risk for carriers of one or more rs1803274(A) alleles, based on a study of 135 Canadian patients * reports ~3.5x increased Alzheimer's risk for carriers of one or more rs1803274(A) alleles, based on a study of 175 patients f...
7 snps
(hide) Breast size
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[GWAS:Breast size]
References:1
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[GWAS:Breast size]
Frequency: 38.9%
References:3
References:3
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[GWAS:Breast size]
References:1
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[GWAS:Breast size]
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[GWAS:Breast size]
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[GWAS:None]
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[GWAS:Breast size]
References:1
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[GWAS:Breast size]
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[GWAS:Breast size]
References:1
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breast size
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[GWAS:Breast size]
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[GWAS:Breast size]
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[GWAS:Breast size]
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breast size [GWAS:Breast cancer]
Frequency: 35.4%
References:1
References:1
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[GWAS:Breast size]
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[GWAS:Breast size]
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[GWAS:Breast size]
19 snps
(hide) Cannabis
Associated with Alcohol Dependence; associated with nicotine dependence (female) Cannabinoid Receptor 1 Gene is Associated with Alcohol Dependence. Alcoholic patients with TGT haplotype (corresponding to rs6454674-rs1049353-rs806368 polymorphisms in this order) were less prone to have AD (p = 0.017). TGC haplotype were more likely to develop AD. Cannabinoid receptor 1 gene association with nicotine dependence. the associations were female specific. Haplotype 1-1-2 of markers rs2023239-rs12720071-rs806368(C) was associated with nicotine dependence and FTND score in the 2 samples (P < .001 and P = .009, respectively).
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risk of the development of substance dependence significantly increased with the number of 'G' alleles at rs6454674 and SNP8 (rs806368);T/T genotypes had significant interaction effects (p = .0003 for comorbid drug dependence (DD) and alcohol dependence (AD), .0002 for DD, and .007 for AD). SNP3 and SNP8 together exerted stronger genetic effects on SD (substance dependence) than either did individually. The peak delta values among all the markers were seen for SNP3 and SNP8 (rs806368) rs806368(C) together with rs1049353(A) or rs1049353(G) make up a haplotype associated with PTSD, with the C-A haplotype somewhat associated (p=0.04) with higher risk of PTSD and the C-G haplotype associated (p=0.01) with a lower risk of PTSD. Alcoholic patients with TGT haplotype (corresponding to rs6454674-r...
Frequency: 54.5%
References:1
References:1
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[GWAS:None]
1.4x higher schizophrenia risk
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rs6277 (957C>T, Pro319Pro) is one of several SNPs in the dopamine receptor DRD2 gene. In a study of 300+ Russian patients with schizophrenia, the rs6277(C) allele was associated with higher risk. From a pooled meta-study (total of 4 other reports plus this one) the allelic odds ratio is 1.42 (CI: 1.26-1.61, p<0.00005), and the genotypic odds ratio for the (C;C) genotype was 1.6 (CI: 1.32-1.95, p<0.00005). Note that rs6275 and rs6277 are only 18bp apart, hence their very tight linkage (r<sup>2</sup>=1). gs278 reflects a gene-gene interaction between this SNP and a NR3A SNP, rs10989591, in which older adults with a particular combination of genotypes at these two (independent) loci are reported to exhibit better episodic memory. C allele associated significantly (p = 0.0...
Frequency: 45.1%
References:1
References:1
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[GWAS:None]
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rs2494732 is a SNP in the AKT1 gene, encoding one of three serine/threonine-protein kinases regulating numerous processes such as cell survival, growth and angiogenesis. Medical conditions that may be linked to the rarer (minor) rs2494732(C) allele include drug response, schizophrenia, and drug-related psychoses, in particuler, cannabis-related psychosis. A case-control study of 489 first-episode psychosis patients concluded that while rs2494732 was not associated with an increased risk of a psychotic disorder, with lifetime cannabis use, or with frequency of use, there was a significant association between psychosis and cannabis use. rs2494732(C;C) individuals with a history of cannabis use had an increased likelihood of a psychotic disorder (odds ratio 2.18, CI: 1.1 - 4.3) when compared ...
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
References:5
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Association of the cannabinoid receptor gene (CNR1) with ADHD and post-traumatic stress disorder. Cannabinoid receptor 1 (CNR1) gene: impact on antidepressant treatment response and emotion processing in major depression. Cannabinoid receptor 1 gene association with nicotine dependence. Cannabinoid type-1 receptor gene polymorphisms are associated with central obesity in a Southern Brazilian population. Evidence for association between polymorphisms in the cannabinoid receptor 1 (CNR1) gene and cannabis dependence. Genetic variation in cannabinoid receptor 1 (CNR1) is associated with derangements in lipid homeostasis, independent of body mass index. Candidate genes for cannabis use disorders: findings, challenges and directions. The implication of CNR1 gene's polymorphisms in the modulatio...
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower COMT enzymatic activity, therefore higher dopamine levels; lower pain threshold, enhanced vulnerability to stress, yet also more efficient at processing information under most conditions *rs4680(G) = Warrior. Val, less exploratory, higher COMT enzymatic activity, therefore lower dopamine levels; higher pain threshold, better stress resiliency, albeit with a modest reduction in executive cognition performance under most conditions Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis; summary at ) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compar...
11 snps
(hide) Cholinesterase Inhibitors
possible increased Alzheimer's risk
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The rs1803274(A) allele encodes a version of the butyrylcholinesterase enzyme known as the K variant; it may also be known as CHE*539T or BCHE*539T. The allele produces a 30% reduction in serum butyrylcholinesterase activity, and it is often co-inherited with the SNP encoding the so-called 'atypical' butyrylcholinesterase, rs1799807. Although not replicated by other studies, some studies have found, at least in certain populations, a possible association between this SNP and risk for Alzheimer's disease (independent of ApoE4 status): * reports ~2x increased Alzheimer's risk for carriers of one or more rs1803274(A) alleles, based on a study of 135 Canadian patients * reports ~3.5x increased Alzheimer's risk for carriers of one or more rs1803274(A) alleles, based on a study of 175 patients f...
0.65x lower risk of ovarian cancer; higher risk of coronary heart disease in some studies; somewhat reduced PON catalytic efficiency
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rs662, also known as Q192R, is a SNP in the PON1 gene. It codes for amino acid 192 of the paraoxonase (PON) protein. Variants of this SNP affect PON catalytic efficiency and are correlated with Heart disease and trait-anxiety scores. The normal form, rs662(A), encodes a glutamine (Q), while the variant, rs662(G)), encodes an arginine (R). . While some populations show an association between this SNP and Heart disease, not all do. Perhaps the most striking finding was reported in Japanese patients with non-insulin dependent diabetes mellitus (NIDDM). NIDDM patients with either one or two rs662(G) alleles had a 9 fold higher risk of coronary heart disease compared with rs662(A;A) NIDDM patients. table of odds for cardiovascular disease outcomes 274 ovarian epithelial carcinoma cases and 452 ...
higher risk for heart disease, diabetic retinopathy
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The snp is suspected of being somewhat confused as an ambiguous flip, because the ReferenceAllele of T has a HapMap freq of 15% in CEU. Also notable is that dbSNP shows RefSNP Alleles: A/C/G/T, and other bits that don't quite fit. While the text below is still of use, it is likely that some of the conclusions are reversed. rs854560, also known as L55M, is a SNP in the PON1 gene. It codes for amino acid 55 (or 54, depending on the numbering) of the paraoxonase (PON) protein. Variants of this SNP affect levels of PON protein and mRNA and are correlated with Heart disease, aspects of Diabetes including diabetic retinopathy, and trait-anxiety scores. The apparently more favorable form, rs854560(T), encodes a methionine and lead to elevated levels of paraoxonase, which is generally a good thing...
normal
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rs705381, also known as -161C/T and -162A/G, is a SNP in the upstream promoter region of the PON1 gene. (The assumption of equivalence between these names is based on the results of searching for rs705381 in the Variant Name Mapper.) In a study of 101 mostly Caucasian patients prescribed the atypical antipsychotic risperidone, carriers of a rs705381(C) allele were less likely to gain significant weight compared to rs705381(T;T) carriers, as assessed by physiogenomic analysis of corresponding weight profiles. Two other SNPs, rs8179183 and rs6837793, were also significantly associated with weight profiles in these patients. In a study of 461 participants in the HERITAGE cohort (172 African-American, 289 Caucasian), the combination of rs705381 with 'PON-126' (RS ID unknown) were found to sign...
4 snps
(hide) Coffee
Magnitude: 2.5
more stimulated by coffee
You appear to have a common genotype in the gene CYP1A2 which metabolizes coffee more slowly than some other forms. The same amount of caffeine will tend to have more stimulating effect on slow metabolizers than on fast metabolizers. Ciprofloxacin is also metabolized by CYP1A2, but is unclear if your genotype should influence its effect.
Carrier of one CYP1A2*1F allele; Slow Caffeine Metabolizer. One copy of the slow caffeine metaboliser SNP, and one copy of the fast version. This makes you more strongly affected by drinking coffee, as caffeine is broken down slower in the liver. Supposedly this increases the risk of heart attacks, although other studies show caffeine is generally good for the heart. It also makes caffeine more effective at preventing Breast Cancer, Alzheimer's Disease, and Parkinson's disease. Too much caffeine will shrink your breasts.
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rs762551, also known as -164A>C or -163C>A, is a SNP encoding the CYP1A2*1F allele of the CYP1A2 gene. For historic reasons, the rs762551(C) allele is considered the wild-type, even though it is the rarer allele in most populations. The rs762551(A) allele is the 'fast metabolizer' allele known as CYP1A2*1F; the (C) allele is by comparison a slower metabolizer of certain substrates (including caffeine). In terms of genotypes, only rs762551(A;A) individuals are considered fast metabolizers. Individuals who are rs762551(A;C) heterozygotes or rs762551(C;C) homozygotes are both considered slow metabolizers. The CYP1A2 gene encodes a member of the cytochrome p450 family of proteins, which metabolize nutrients and drugs. One well known substrate of CYP1A2 is caffeine; individuals who are ca...
Able to taste bitterness.
Normal tasting ability for bitterness. This makes turnip, cabbage, brussels sprouts, broccoli, and other cruciferous vegetables taste more interesting and less horribly bland. Coffee and dark beers also tastes more bitter. You can taste propylthiouracil (PROP), PTC, and related chemicals. On the other hand, you can't taste the unpleasant bitterness of the tropical fruit from the Bignay tree, it will taste sweet to you. You probably eat healthier.
Associated with (slightly) increased coffee consumption
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rs6968865 is a SNP located near the aryl hydrocarbon receptor AHR gene on ch 7p21. A meta-analysis of four GWAS studies of coffee consumption among a total of ~8,000 coffee drinkers of European ancestry found that the rs6968865(T) was strongly associated with increased consumption (p = 2.3 x 10e-11). The estimated effect was an increase of 0.2 cups a day per allele for both this SNP and one other (rs2472297).
Can taste bitter. Normal tasting ability for bitterness. This makes turnip, cabbage, brussels sprouts, broccoli, and other cruciferous vegetables taste more interesting and less horribly bland. Coffee and dark beers also tastes more bitter. You can taste propylthiouracil (PROP), PTC, and related chemicals. On the other hand, you can't taste the unpleasant bitterness of the tropical fruit from the Bignay tree, it will taste sweet to you. You probably eat healthier.
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rs713598 is one of three SNPs that form the main haplotypes behind the ability to perceive as bitter the taste of the compound phenylthiocarbamide (PTC) and similar molecules in foods (like cabbage and raw broccoli) or drinks (like coffee and dark beers). The rs713598(G) allele, in the orientation shown in dbSNP, is the 'tasting' allele, and it is dominant to the 'non-tasting' allele rs713598(C), so having one copy is enough to have the bitter tasting ability. If you are a 'taster', you're also likely to carry at least one rs10246939(C) and one rs1726866(C) allele since, along with rs713598(G), these three SNPs form the most common tasting haplotype. If you lack these alleles, you're quite likely (~80%) to be a non-taster of bitterness, meaning that foods that may taste bitter to others ta...
Magnitude: 0.1
References:10
References:10
can taste bitter
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rs10246939 is one of three SNPs that form the main haplotypes behind the ability to perceive as bitter the taste of the compound phenylthiocarbamide (PTC) and similar molecules in foods (like cabbage and raw broccoli) or drinks (like coffee and dark beers). The rs10246939(C) allele, in the orientation shown in dbSNP, is the 'tasting' allele, and it is dominant to the 'non-tasting' allele rs10246939(T), so having one copy is enough to have the bitter tasting ability. If you are a 'taster', you're also likely to carry at least one rs713598(G) and one rs1726866(C) allele since, along with rs10246939(C), these three SNPs form the most common tasting haplotype. If you lack these alleles, you're quite likely (~80%) to be a non-taster of bitterness, meaning that foods that may taste bitter to oth...
can taste bitter
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rs1726866 is one of three SNPs that form the main haplotypes behind the ability to perceive as bitter the taste of the compound phenylthiocarbamide (PTC) and similar molecules in foods (like cabbage and raw broccoli) or drinks (like coffee and dark beers). The rs1726866(C) allele is the 'tasting' allele, and it is dominant to the 'non-tasting' allele rs1726866(T), so having one copy is enough to have the bitter tasting ability. If you are a 'taster', you're also likely to carry at least one rs713598(G) and one rs10246939(C) allele since, along with rs1726866(C), these three SNPs form the most common tasting haplotype. If you lack these alleles, you're quite likely (~80%) to be a non-taster of bitterness, meaning that foods that may taste bitter to others taste far less bitter to you. (C;C)...
None
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Variation at this SNP, rs5751876, also referred to as 1976C>T or 1976T>C, appears to influence how an individual responds to moderate levels (150mg) of caffeine. T/T carriers displaying significantly increased subjective levels of anxiety after consumption. However a PharmGKB variant annotation suggests it is (C;C) genotypes who are more sensitive to caffeine. rs5751876 is not associated with how much coffee one drinks, though, nor with risk for Parkinson's disease, based on a study of 1,200 subjects. 'rs2298383 shows functional potential based on in silico analyses and might therefore represent the true underlying causal variant'
2 genosets 6 snps
(hide) Coriell Personalized Medicine Collaborative
1.3x higher risk of ER+ breast cancer
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rs2981582 in the FGFR2 gene was one of the four strongest associations found in a genome-wide association study (GWAS) of over 4,000 breast cancer samples. The T allele was more strongly related to ER-positive (per-allele odds ratio 1.31 (CI: 1.27-1.36)) than ER-negative (odds ratio 1.08 (CI:1.03-1.14)) disease (p for heterogeneity = 10(-13)). While on its own still of fairly small effect, this was the most significant of 7 SNPs to help estimate risk of breast cancer. Family history and/or BRCA1 or BRCA2 testing status are more significant factors, which were not part of this panel. Based on a study of 1,049 Chinese breast cancer patients, carriers of risk alleles at three SNPs (rs2981582, rs1219648 and rs2420946) were at 1.36x increased risk for breast cancer (CI: 1.13-1.62, p = 0.001). A...
poorer metabolizer of several popular medicines; patients prescribed Plavix get less benefit, and have higher risk for adverse cardiovascular events
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rs4244285 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*2 variant. This variant is the most common reason for poor metabolism of compounds like mephenytoin (an anti-convulsant), some antidepressants, the anti-platelet drug Plavix, and some drugs used for ulcer conditions of various types. The risk allele is rs4244285(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (trade name Prevacid). In Caucasians, SNPs in CYP2C19 are relatively rare (in contrast to SNPs in CYP2D6), but SNPs in this gene are common in Asians. Ulcer treatment with omeprazole to reduce Helicobacter pyl...
1.5x increased risk for CAD 1.5x higher risk for coronary artery disease
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rs1333049 has been reported in a large study to be associated with heart disease, in particular, coronary artery disease. The risk allele (oriented to the dbSNP entry) is most likely (C); the odds ratio associated with heterozygotes is 1.47 (CI 1.27-1.70), and for homozygotes, 1.9 (CI 1.61-2.24). This SNP has also been reported to have the highest association of any SNP studied in a subsequent experiment conducted with the resources of the German MI [Myocardial Infarction] Family Study. The initial studies were conducted on Caucasian populations. A subsequent study of Japanese and Korean patients has also found rs1333049 to be associated with increased coronary artery disease risk, with roughly similar odds ratios. '''Further reading (with comments)''' - A long-term study of a cohort of 76...
1.3x increased risk for type-2 diabetes
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The accuracy of claims about this snp are called into question by table 1 of discusses the process of including this snp into Coriell and raises some doubt about the value of its inclusion. rs7754840 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.28 (CI: 1.17-1.41, p = 4.5 x 10e-7) type-2 diabetes Carriers of the (C;G) and (C;C) genotypes of rs7754840 had 11% and 24% lower first-phase insulin release in an IVGTT compared to that in carriers of the (G;G) genotype (P=0.002). The C allele was also associated with higher glucose area under the curve in an OGTT (P=0.016). rs7754840 type-2 diabetes Ashkenazi Jewish population shows an even stronger effect for rs7754840 than the general Caucasian population, based on 1,131 cases versus 1,147 co...
1.3x risk of prostate cancer; aspirin reduces risk of colorectal cancer Increased risk for prostate cancer and in women other types of cancer. Aspirin has been reported to help reduce the risk somewhat when taken by carriers of this genotype.
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rs6983267 is a SNP on chromosome 8q24, associated with increased risk for several cancers, particularly prostate cancer. In studies dividing the 8q24 region, this SNP falls in region 3. This SNP has also been reported to influence the cancer-risk-decreasing effect of aspirin. In a study of over 3,600 Caucasians with prostate cancer, rs6983267 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On their own, the rs6983267(G;G) and (G;T) risk genotypes yield an odds ratio for developing prostate cancer of 1.37 (CI: 1.18-1.59, p=3.4-10e-5) and may account for 22.2% of population attributable risk. The increased risk of developing prostate cancer associated with rs6983267 now appears to be independent of the risk associated with its close neig...
1.5x increased bladder cancer risk
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rs9642880 is a SNP located in chromosome region 8q24, a region that has been linked to prostate, breast, and colon cancer. A study ultimately totaling over 4,000 bladder cancer patients of European ancestry (and 40,000 controls) concluded that individuals carrying two copies of rs9642880(T) were at 1.49x increased risk (allele-specific odds ratio = 1.22, p = 9 x 10e-12) for the disease. This SNP was not associated, however, with risk for prostate, breast, or colon cancer. Another study in Chinese populations found similar results in regard to bladder cancer. rs9642880(T;T) estimated risk of developing 1.49 times that of noncarriers. 1,803 urinary bladder cancer cases and 34,336 controls. No association with prostate, colorectal and breast cancers. In contrast to GSTM1 SNPs, the rs9642880(T...
Magnitude: 2
Frequency: 43.1%
References:13
Frequency: 43.1%
References:13
CYP2C19*17 ultra fast metabolizer; drug metabolism effects; also 0.77x decreased breast cancer risk
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rs12248560(T) defines the CYP2C19*17 allele, an ultra fast metabolizer phenotype of the CYP2C19 gene. CYP2C19*17 is likely to lead to less effective drug treatment by, for example, proton pump inhibitors (such as omeprazole) and antidepressants. On the other hand, cancer patients who are CYP2C19*17 carriers are more likely to benefit from tamoxifen treatment, presumably because they break it down more rapidly into the antiestrogenic metabolites endoxifen and 4-hydroxytamoxifen. A study of 1,000+ breast cancer patients showed a 0.77x decreased risk of breast cancer for carriers of a CYP2C19*17 allele (CI: 0.65-0.93, p = 0.005). Analysis of a subgroup of such carriers who were using hormone therapy for ten years or longer showed an even stronger effect (odds ratio 0.57, CI: 0.39-0.83, p = 0....
1.4x higher risk of lupus increased risk of Systemic lupus erythematosus.
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CPMC uses this to indicate increased risk of Systemic lupus erythematosus. [GWAS:Systemic lupus erythematosus]
non-protective against testicular cancer
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23andMe blog each rs4624820(G) increases the odds of testicular cancer by 2.5x. <p><br> As reported by the CPMC, relative to men who are rs995030(A;A), men who are rs995030(A;G) have a 0.38 relative risk, and those who are (G;G) have a 0.15 relative risk. Association of genetic markers within the KIT and KITLG genes with human male infertility. Common variation in KITLG and at 5q31.3 predisposes to testicular germ cell cancer. [OMIM:?] [GWAS:Testicular germ cell tumor]
None
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rs2108622 is a SNP in the cytochrome P450, family 4, subfamily F, polypeptide 2 CYP4F2 gene. In the males rs2108622(G) was significantly higher in cerebral infarction patients (P = 0.025) A study of Italian patients concluded that rs2108622(T;T) patients require 5.49 mg/day of warfarin versus 2.93 mg/day for (C;C) patients. Analysis of variance indicates that about 7% of mean weekly warfarin dose variance is explained by CYP4F2 genotype. A study of 370 Brazilian ('admixed') patients concludes that prospective CYP4F2 genotyping is of little value to these patients, presumably due to ethnic-based differences. [PharmGKB:Curated Risk or phenotype-associated allele: no allelic association. Phenotype: Improved pharmacogenetic algorithm-based warfarin dosing. Study size: 370. Study population/et...
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A genome-wide association study of pulmonary function measures in the Framingham Heart Study. Hedgehog-interacting protein is a COPD susceptibility gene: the Rotterdam Study. [PharmGKB:Non-Curated GWAS results: A Genome-Wide Association Study in Pulmonary Disease, Chronic Obstructive (COPD): Identification of Two Major Susceptibility Loci. (Initial Sample Size: 823 cases, 810 controls; Replication Sample Size: 2,840 family members, 389 cases, 472 controls); (Region: 4q31.22; Reported Gene(s): HHIP; Risk Allele: rs1828591-?); (p-value= 0.0000001).This variant is associated with Pulmonary Disease, Chronic Obstructive.] [GWAS:Chronic Obstructive Pulmonary Disease]
normal
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rs401681 is a SNP in the CLPTM1-like CLPTM1 gene. The following studies span several types of cancer, and over 30,000 cases and 45,000 controls. deCODE press release reports rs401681 linked to basal cell carcinoma and many cancers for individuals with shorter telomeres, whereas those with long telomeres are at greater risk of melanoma. Neighboring rs2736098 also increases risk of cancer by affecting telomerase reverse transcriptase. The risk of these different cancers conferred by these two SNPs appears to be independent. 23andMe blog rs2736098 and rs401681 linked to many cancers, including susceptibility to pancreatic cancer However, a very large study (encompassing thousands of cases and controls) found no association between rs401681 and either (1) mean telomere length, or, (2) breast c...
Magnitude: 0
Frequency: 26.5%
Repute:Good
References:5
Frequency: 26.5%
Repute:Good
References:5
normal/common in clinvar Found in 56% of all Caucasians on average, this genotype leads to a relative risk of 1.00, which is the most common risk, for late-onset (adult) asthma.
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rs1837253 is a SNP found a bit upstream of the thymic stromal lymphopoietin TSLP gene on chromosome 5. The TSLP protein plays a role in inflammation of cells in the trachea and alveoli therefore may have a causative role in certain types of asthma. The rs1837253(T) allele has been found to reduce the risk of developing late-onset (adult) asthma in several studies, and it is recognized by the CPMC Study as one they report to their participants. [GWAS:None]
15 snps
(hide) CYP1A2
Magnitude: 2.5
more stimulated by coffee
You appear to have a common genotype in the gene CYP1A2 which metabolizes coffee more slowly than some other forms. The same amount of caffeine will tend to have more stimulating effect on slow metabolizers than on fast metabolizers. Ciprofloxacin is also metabolized by CYP1A2, but is unclear if your genotype should influence its effect.
Carrier of one CYP1A2*1F allele; Slow Caffeine Metabolizer. One copy of the slow caffeine metaboliser SNP, and one copy of the fast version. This makes you more strongly affected by drinking coffee, as caffeine is broken down slower in the liver. Supposedly this increases the risk of heart attacks, although other studies show caffeine is generally good for the heart. It also makes caffeine more effective at preventing Breast Cancer, Alzheimer's Disease, and Parkinson's disease. Too much caffeine will shrink your breasts.
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rs762551, also known as -164A>C or -163C>A, is a SNP encoding the CYP1A2*1F allele of the CYP1A2 gene. For historic reasons, the rs762551(C) allele is considered the wild-type, even though it is the rarer allele in most populations. The rs762551(A) allele is the 'fast metabolizer' allele known as CYP1A2*1F; the (C) allele is by comparison a slower metabolizer of certain substrates (including caffeine). In terms of genotypes, only rs762551(A;A) individuals are considered fast metabolizers. Individuals who are rs762551(A;C) heterozygotes or rs762551(C;C) homozygotes are both considered slow metabolizers. The CYP1A2 gene encodes a member of the cytochrome p450 family of proteins, which metabolize nutrients and drugs. One well known substrate of CYP1A2 is caffeine; individuals who are ca...
References:2
carrier of one CYP1A2*1D allele
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rs35694136, also known as -2467delT, is a SNP in the CYP1A2 gene. The rs35694136(-) allele defines the CYP1A2*1D variant.
References:1
1 genoset 4 snps
(hide) CYP2A6
Magnitude: 1
References:4
References:4
Reduced CYP2A6 metabolism; impaired nicotine metabolism?
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rs28399433, also known as -47A>C, is a SNP in the CYP2A6 gene. CYP2B6 (c.516G-->T) and CYP2A6 (*9B and/or *17) polymorphisms are independent predictors of efavirenz plasma concentrations in HIV-infected patients. CYP2B6 variants and plasma efavirenz concentrations during antiretroviral therapy in Port-au-Prince, Haiti. [PharmGKB:In-Depth This variant results in decreased enzyme expression and activity, which affects nicotine and coumarin metabolism; part of the CYP2A6*9 haplotype.]
1 snp
(hide) CYP2C19
CYP2C19 Intermediate Metabolizer
CYP2C19 Intermediate Metabolizer. Your body breaks down some medicines at a slightly slower than normal rate (which is represented by gs150). Individuals with gs152 genotypes have even slower metabolism. *anti-epileptics (such as diazepam, phenytoin, and phenobarbitone) *anti-depressants (such as amitriptyline and clomipramine) *anti-platelet drug clopidogrel (Plavix) *anti-ulcer proton pump inhibitors like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (Prevacid) *hormones (estrogen, progesterone).
poorer metabolizer of several popular medicines; patients prescribed Plavix get less benefit, and have higher risk for adverse cardiovascular events
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rs4244285 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*2 variant. This variant is the most common reason for poor metabolism of compounds like mephenytoin (an anti-convulsant), some antidepressants, the anti-platelet drug Plavix, and some drugs used for ulcer conditions of various types. The risk allele is rs4244285(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (trade name Prevacid). In Caucasians, SNPs in CYP2C19 are relatively rare (in contrast to SNPs in CYP2D6), but SNPs in this gene are common in Asians. Ulcer treatment with omeprazole to reduce Helicobacter pyl...
Magnitude: 2
Frequency: 43.1%
References:13
Frequency: 43.1%
References:13
CYP2C19*17 ultra fast metabolizer; drug metabolism effects; also 0.77x decreased breast cancer risk
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rs12248560(T) defines the CYP2C19*17 allele, an ultra fast metabolizer phenotype of the CYP2C19 gene. CYP2C19*17 is likely to lead to less effective drug treatment by, for example, proton pump inhibitors (such as omeprazole) and antidepressants. On the other hand, cancer patients who are CYP2C19*17 carriers are more likely to benefit from tamoxifen treatment, presumably because they break it down more rapidly into the antiestrogenic metabolites endoxifen and 4-hydroxytamoxifen. A study of 1,000+ breast cancer patients showed a 0.77x decreased risk of breast cancer for carriers of a CYP2C19*17 allele (CI: 0.65-0.93, p = 0.005). Analysis of a subgroup of such carriers who were using hormone therapy for ten years or longer showed an even stronger effect (odds ratio 0.57, CI: 0.39-0.83, p = 0....
increased risk of cannabis dependence, lower (normal) cancer risk '''Association between ABCB1 C3435T polymorphism and increased risk of cannabis dependence.''' (2009). Patients with cannabis dependence (n=40) had a significantly higher 3435C allele frequency (62.5% versus 43.8% respectively, P=0.017) and CC genotype (50% versus 20%, P=0.005, OR=4.00 [1.50-10.60). The CC genotype was independently associated with cannabis dependence. This is the first time a significant specific genetic marker has been shown in cannabis dependence. ABCB1 polymorphisms may alter Delta9THC distribution, its psychoactive effects and individual vulnerability to dependence.
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rs1045642, also known as C3435T, is a SNP located in the ABCB1 gene. It is often studied in conjunction with rs2032582. C3435T has been mentioned by: * A 'Silent' Polymorphism in the MDR1 Gene Changes Substrate Specificity (for example, to verapamil) * (R)-lansoprazole (Prevacid) concentrations are significantly increased in CYP2C19 extensive metabolizers with ABCB1 C3435T C allele. * In a Korean population, plasma concentrations of fexofenadine (Allegra) were 17% lower in 2677AA/3435CC subjects and 47% higher in the 2677TT/3435TT subjects compared to 2677GG/3435CC subjects. * In contrast, in this study no association was observed between the C3435T polymorphism and fexofenadine plasma or urine concentrations in a German Caucasian population. * A meta-analysis including 9 case-control stud...
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[GWAS:Blood metabolite levels]
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[GWAS:Migraine]
carrier of one CYP2C19*2B allele
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The rs17878459(C) SNP defines the CYP2C19 allele known as CYP2C19*2B, or as E92D.
References:1
Frequency: 22.7%
References:1
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[GWAS:Acenocoumarol maintenance dosage]
1 genoset 8 snps
(hide) CYP2C9
References:2
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[Distribution of variant alleles association with warfarin pharmacokinetics and pharmacodynamics in the Han population in China].
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associations with higher warfarin dose, namely, VKORC1-8191 (rs61162043, P = 0.0041) and 18786 in CYP2C9 (rs7089580, P = 0.035) independent of the previous associations with these genes
4 snps
(hide) CYP2D6
poorer metabolizer of several popular medicines; patients prescribed Plavix get less benefit, and have higher risk for adverse cardiovascular events
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rs4244285 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*2 variant. This variant is the most common reason for poor metabolism of compounds like mephenytoin (an anti-convulsant), some antidepressants, the anti-platelet drug Plavix, and some drugs used for ulcer conditions of various types. The risk allele is rs4244285(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (trade name Prevacid). In Caucasians, SNPs in CYP2C19 are relatively rare (in contrast to SNPs in CYP2D6), but SNPs in this gene are common in Asians. Ulcer treatment with omeprazole to reduce Helicobacter pyl...
Magnitude: 2
CYP2D6*41
CYP2D6*41 decreased metabolism
Magnitude: 2
CYP2D6*2
CYP2D6*2 normal metabolism
Carrier of at least one CYP2D6 variants (non-CYP2D6*1)
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rs1135840, also known as 4180G>C or S486T, is a SNP in the CYP2D6 gene. The wild type (normal) allele at this SNP is (G). The (C) variant indicates the presence of a non-wild type CYP2D6 variant, but it appears in many different variants so it can not be used to determine the presence of any particular variant. Please be careful when interpreting results for this SNP as it is in dbSNP and SNPedia in minus orientation where the risk allele is C, but test results are usually in plus orientation where the risk allele is G. This SNP has an ambiguous flip which can make this very confusing. Polymorphisms affecting gene transcription and mRNA processing in pharmacogenetic candidate genes: detection through allelic expression imbalance in human target tissues. [PharmGKB:Curated Risk or phenot...
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rs7439366, also known as Y268H, is a SNP in the UGT2B7 gene encoding the 2B7 UDP-Glucuronosyltransferase, active primarily in the liver. The rs7439366(C) allele encodes a histidine (H) at amino acid 268, and the (T) allele encodes a tyrosine (Y). Most publications refer to the histidine as the wild-type (more common) allele. In a study of glucuronidation activity of human livers, rs7439366(T;T) individuals had 28% lower activity than rs7439366(C;C) individuals with respect to O-glucuronidation of tamoxifen metabolites 4-OH-tamoxifen and endoxifen. The authors suggest this may help explain interindividual variability (beyond CYP2D6 variation) in tamoxifen metabolism - and therefore the effectiveness of tamoxifen in reducing breast cancer recurrence. [PharmGKB:Curated Risk or phenotype-asso...
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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The 1661G>C variation in CYP2D6. Involved in a number of decreased and non-functioning CYP2D6 variants. This SNP does not yet appear to be common in consumer tests.
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
References:5
carrier of one CYP2D6*41 allele
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rs28371725, also known as 2988G>A, is a SNP in the CYP2D6 gene. The rs28371725(A) allele defines the CYP2D6*41 variant, which has decreased activity. 23andMe also has SNP i4001476 at the same position. [PharmGKB:In-Depth This variant is part of the CYP2D6*41 IM haplotype. Plasma concentrations of metoprolol were shown to be were 4.9-fold higher in the PMs, with greater reductions in heart rate, diastolic blood pressure, and mean arterial pressure in PMs than in non-PMs.]
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
a common variant
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The wild type (normal) allele at this SNP is (G). The (A) variant indicates the presence of a non-wild type CYP2D6 variant, but it appears in many different variants so it can not be used to determine the presence of any particular variant. Inheriting a normal number of copies of this allele results in CYP2D6 function that is indistinguishable from wild-type (normal) activity. However, this variant has been seen present in higher copy numbers, and in these cases, can result in the ultrafast metabolizer phenotype . [PharmGKB:In-Depth Risk or phenotype-associated allele: T. Phenotype: The CYP2D6*2A haplotype was associated with lower incidence of breast cancer on tamoxifen compared to placebo in a prevention study. The CYP2D6*2A allele may be associated with increased efficacy of tamoxifen....
a common variant
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rs1080985 is a SNP near the CYP2D6 gene. Depending on the publication source, it may be called '-1584C/G' or '1496C>G' or the like. The wild type (normal) allele at this SNP is (C). The (G) variant indicates the presence of a non-wild type CYP2D6 variant, but it appears in many different variants so it can not be used to determine the presence of any particular variant. The rs1080985(G) allele defines the CYP2D6*2A variant, which has been reported to have relatively normal function yet in some cases may also lead to the intermediate metabolism phenotype. Please be careful when interpreting results for this SNP as it is in dbSNP and SNPedia in minus orientation where the risk allele is G, but test results are usually in plus orientation where the risk allele is C. This SNP has an ambiguo...
common
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rs1080983 is a SNP near the 5' end of the CYP2D6 gene. Little is known of the significance of either allele.
2 genosets 32 snps
(hide) CYP2E1
carrier of one CYP2E1*7_-71G>T allele
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rs6413420 is a SNP in the CYP2E1 gene. The rs6413420(T) allele defines the CYP2E1*7_-71G>T variant.
normal
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rs915909 is a SNP in the CYP2E1 gene. The rs915909(T) allele defines the CYP2E1_6498C>T(I321I) variant.
3 snps
(hide) CYP3A5
1.6x higher overall CYP3A activity
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rs1057868, also known as A503V, is a relatively common variant defining the POR*28 allele of the P450 (cytochrome) oxidoreductase POR gene. The POR gene encodes a protein involved in electron transport of cytochrome p450 enzymes such as CYP3A4, CYP3A5 and CYP3A7. A study of 251 individuals from two independent studies (182 patients treated with methadone and 69 patients with clozapine) for CYP3A activity found that CYP3A SNPs themselves did not predict particularly well inter-individual variability in overall CYP3A activity. However, rs1057868(T;T) individuals had a 1.6x increased CYP3A activity compared to rs1057868(C) carriers (n=182, p=0.004), and the finding was replicated in a second independent dataset. The authors conclude that this POR gene SNP is a better predictor of overall CYP3...
1 snp
(hide) DCDC2
Slightly increased dyslexia risk
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Rs807701, a SNP in the DCDC2 gene, is in a region that crops up in several independent studies as likely to associated with dyslexia. The risk allele in the Caucasian populations studied is (C). One study reports that the odds ratio for rs807701 genotypes increases if calculated from subsets of more severely dyslexic individuals as compared to more heterogenous, larger groups of dyslexic individuals. The genotype relative risk (GRR) for rs807701(C;C) increased from 1.88 (95% CI 0.89-3.97; P=.058) for the larger group up to 5.04 (95% CI 1.35-18.88; P=.002) for the most severely affected group. Combined with another SNP marker in the DCDC2 gene, rs793862, the (haplotype) GRR also increased for the homozygous haplotype rs793862(A)-rs807701(C), from 4.11 (95% CI 2.77-6.08; P<.0001) for the ...
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[OMIM:?]
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Strong genetic evidence of DCDC2 as a susceptibility gene for dyslexia.
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[OMIM:?]
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Strong genetic evidence of DCDC2 as a susceptibility gene for dyslexia. [OMIM:?]
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[OMIM:?]
8 snps
(hide) Doi:10.1186/1471-2156-10-88
Carrier of one CYP1A2*1F allele; Slow Caffeine Metabolizer. One copy of the slow caffeine metaboliser SNP, and one copy of the fast version. This makes you more strongly affected by drinking coffee, as caffeine is broken down slower in the liver. Supposedly this increases the risk of heart attacks, although other studies show caffeine is generally good for the heart. It also makes caffeine more effective at preventing Breast Cancer, Alzheimer's Disease, and Parkinson's disease. Too much caffeine will shrink your breasts.
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rs762551, also known as -164A>C or -163C>A, is a SNP encoding the CYP1A2*1F allele of the CYP1A2 gene. For historic reasons, the rs762551(C) allele is considered the wild-type, even though it is the rarer allele in most populations. The rs762551(A) allele is the 'fast metabolizer' allele known as CYP1A2*1F; the (C) allele is by comparison a slower metabolizer of certain substrates (including caffeine). In terms of genotypes, only rs762551(A;A) individuals are considered fast metabolizers. Individuals who are rs762551(A;C) heterozygotes or rs762551(C;C) homozygotes are both considered slow metabolizers. The CYP1A2 gene encodes a member of the cytochrome p450 family of proteins, which metabolize nutrients and drugs. One well known substrate of CYP1A2 is caffeine; individuals who are ca...
Common variant. Slightly shorter lifespan. Chemotherapy is less effective. Accelerated lung decline in smokers. African Americans have 2.15x risk of dying from colo-rectal cancer.
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This SNP, a variant in the TP53 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the G allele encodes an arginine at position 72 of the protein (where there's normally a proline), and the SNP is commonly called the Arg72 variant, although P72R and Arg72Pro are also common in the literature. Minor allele homozygotes, i.e. rs1042522(C;C) genotypes, live on average 3 years longer than major allele (G;G) homozygotes, based on a study of 9,200+ Danish individuals. The increased longevity is speculated to be related to the i...
1.12x increased risk for cutaneous melanoma
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rs13181 is a SNP of the XPD/ERCC2 gene. A meta-analysis of 20 studies, comprising 2,308 cases, ultimately concluded that the rs13181(G) allele is associated with increased cutaneous melanoma risk (odds ratio 1.12, CI: 1.03-1.21, p = 0.01; population attributable risk = 9.6%). Polymorphisms in XPD and TP53 and mutation in human lung cancer. Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method. ERCC1 and ERCC2 polymorphisms and adult glioma. [Correlation of genetic polymorphisms in nucleotide excision repair system to sensitivity of advanced non-small cell lung cancer patients to platinum-based chemotherapy]. Bladder cancer predisposition: a multigenic approach to DNA-repair and cell-cycle-control genes. Risk of non-Hodgk...
Generally European; Light skin; Possibly an increased risk of melanoma This SNP is associated with skin, hair, and eye colour, and risk of melanoma. Individuals with the G;G genotype are generally of European descent and have fair skin. In a population-based case-control study investigating a number of pigmentation-related SNPs and their correlation with cutaneous malignant melanoma (CMM) in a Caucasian Australian population, rs16891982 (variant F374L) was found to be associated with odds ratios of 3.44, 2.86, 1.68, and 1.68 for all study subjects (1,738 CMM cases and 4,517 controls); subjects with northern European ancestry (1,438 cases and 3,098 controls); northern European subjects adjusted for hair, eye, and skin colour; and northern European subjects adjusted for the MC1R genotype, r...
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This snp influences skin pigmentation. The allele p.L374F indicates light-skinned european ancestry c.1122C>G, p.Phe374Leu (NCBI dbSNP rs16891982) in SLC45A2 was associated with protection from malignant melanoma (OR, 0.41; 95% CI, 0.24-0.70; P=0.008 after adjustment for multiple testing) An association study conducted on a population of European origin concluded that the rare (in Europeans, at least) allele L374, i.e. rs16891982(C) in dbSNP orientation, significantly increases the possibility of having black hair color, with an odds ratio of around 7. This population-based case-control study investigated a number of pigmentation-related SNPs and their correlation with cutaneous malignant melanoma (CMM) in an Australian population. rs16891982 (variant F374L) was found to be associated w...
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Influences appearance The A allele of rs1042602 is associated with the absence of freckles [PharmGKB:Non-Curated GWAS Results: A genomewide association study of skin pigmentation in a South Asian population (Initial Sample Size: 363 with maxL* < 56 and 374 with maxL* > 63; 20% tails of distribution; Replication Sample Size: 116 low maxL*, 115 high maxL* individuals). This variant is associated with skin pigmentation by reflectance spectroscopy.] [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 3; SHEP3] [GWAS:Freckles] [GWAS:Skin pigmentation by reflectance spectroscopy]
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DNA polymorphism and risk of esophageal squamous cell carcinoma in a population of North Xinjiang, China.
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Influences appearance gnxp A genomewide association study of skin pigmentation in a South Asian population. Complex signatures of selection for the melanogenic loci TYR, TYRP1 and DCT in humans.
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[PharmGKB:Curated Risk or phenotype-associated allele: Not specified. Phenotype: This SNP was associated with clearance of docetaxel. Study size: 31. Study population/ethnicity: Patients with Non-Small-Cell Lung Carcinoma. Significance metric(s): p = 0.0097 (ANOVA); p = 0.0013 (QMIS); p = 0.0040 (KW) Type of association: PK.]
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Bisphosphonate-related osteonecrosis of the jaw is associated with polymorphisms of the cytochrome P450 CYP2C8 in multiple myeloma: a genome-wide single nucleotide polymorphism analysis. [OMIM:MYELOMA, MULTIPLE]
References:2
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[PharmGKB:Curated Variant was identified in a cohort of 54 Japanese individuals, who were administered the anti-arrhythmic drug amiodarone. (HapMap SNP)]
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A three-single-nucleotide polymorphism haplotype in intron 1 of OCA2 explains most human eye-color variation. Three genome-wide association studies and a linkage analysis identify HERC2 as a human iris color gene.
blue/gray eyes less likely
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rs7495174 is located in intron 1 of the OCA2 gene. The (A) allele (in dbSNP orientation) is associated with blue or green eye color in Caucasians. . This SNP is 1 of 3 SNPs defining a haplotype that has been studied for association with eye color. The full details on the correspondence between the haplotype and eye color can be found on the OCA2 page. [PharmGKB:Curated A haplotype containing rs11855019, rs6497268 and rs7495174 was highly associated with eye color, hair color and skin pigmentation in a mostly Northern European twin study.] [OMIM:OCA2 GENE]
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[OMIM:DYSTROBREVIN-BINDING PROTEIN 1; DTNBP1]
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prostate cancer treatment response rs2279115 and rs7121 Complex haplotype structure of the human GNAS gene identifies a recombination hotspot centred on a single nucleotide polymorphism widely used in association studies. Polymorphism in maternal LRP8 gene is associated with fetal growth. Differential allelic expression in the human genome: a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression. PTHR1 mutations associated with Ollier disease result in receptor loss of function. Functional genetic polymorphisms and female reproductive disorders: Part I: Polycystic ovary syndrome and ovarian response. A sensitive functional assay reveals frequent loss of genomic imprinting in human placenta. Association of the GNAS locus with severe malaria. Dev...
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[GWAS:None]
26 snps
(hide) DRD4
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[PharmGKB:Curated This variant in exon 3 of DRD4 along with 3 other SNPs near DRD4 (4 SNP haplotype: rs3758653; rs916457; rs762502; rs11246226) is associated with tardive dyskinesia in male schizophrenia patients.]
1 snp
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poorer metabolizer of several popular medicines; patients prescribed Plavix get less benefit, and have higher risk for adverse cardiovascular events
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rs4244285 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*2 variant. This variant is the most common reason for poor metabolism of compounds like mephenytoin (an anti-convulsant), some antidepressants, the anti-platelet drug Plavix, and some drugs used for ulcer conditions of various types. The risk allele is rs4244285(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (trade name Prevacid). In Caucasians, SNPs in CYP2C19 are relatively rare (in contrast to SNPs in CYP2D6), but SNPs in this gene are common in Asians. Ulcer treatment with omeprazole to reduce Helicobacter pyl...
homozygous for C677T of MTHFR = 10-20% efficiency in processing folic acid = high homocysteine, low B12 and folate levels This is the homozygous form of the C677T allele for the MTHFR gene. It is found in approximately * 15% of Hispanic Americans * 12% of Caucasian Americans * 12% of Japanese * 6% of Germans * 3% of Asians * 2% of African Americans * 1% of Sub-Saharan Africans Numerous health effects are associated with this variant. * Hyperhomocysteinemia and neurologic disorders: a review. (2014). A review. Certain genetic factors also cause elevated homocysteine levels, such as C667T substitution of the gene encoding methylenetetrahydrofolate reductase. Elevated homocysteine has been observed in several medical conditions, such as cardiovascular disorders, atherosclerosis, myocardial i...
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer ** renal cancer * cleft lip and cleft palate * coronary artery disease * dementia * depression * hyperhomocysteinemia * migraine * neural tube d...
Carrier of one CYP1A2*1F allele; Slow Caffeine Metabolizer. One copy of the slow caffeine metaboliser SNP, and one copy of the fast version. This makes you more strongly affected by drinking coffee, as caffeine is broken down slower in the liver. Supposedly this increases the risk of heart attacks, although other studies show caffeine is generally good for the heart. It also makes caffeine more effective at preventing Breast Cancer, Alzheimer's Disease, and Parkinson's disease. Too much caffeine will shrink your breasts.
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rs762551, also known as -164A>C or -163C>A, is a SNP encoding the CYP1A2*1F allele of the CYP1A2 gene. For historic reasons, the rs762551(C) allele is considered the wild-type, even though it is the rarer allele in most populations. The rs762551(A) allele is the 'fast metabolizer' allele known as CYP1A2*1F; the (C) allele is by comparison a slower metabolizer of certain substrates (including caffeine). In terms of genotypes, only rs762551(A;A) individuals are considered fast metabolizers. Individuals who are rs762551(A;C) heterozygotes or rs762551(C;C) homozygotes are both considered slow metabolizers. The CYP1A2 gene encodes a member of the cytochrome p450 family of proteins, which metabolize nutrients and drugs. One well known substrate of CYP1A2 is caffeine; individuals who are ca...
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[PharmGKB:Curated This SNP at chromosome 9 is significantly associated with HNRPD expression (located on chromosome 4), and daunorubicin IC50 in CEU population using International HapMap cell lines.]
~10% more likely to respond to citalopram
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rs1954787, located in an intron of the GRIK4 gene, was found to be associated with a somewhat increased rate of successful response to treatment of depression with the drug citalopram. From the abstract of this article: 'The effect size of (this) GRIK4 marker alone was modest, but homozygote carriers of the treatment-response-associated marker alleles of both the GRIK4 and HTR2A (see rs7997012) genes were 23% less likely to experience nonresponse to (citalopram) treatment relative to participants who did not carry any of these marker alleles.' * See also Anxiety Blog posting [PharmGKB:Curated A study in 1,816 eligible patients from the STAR*D cohort found that genetic variation in a kainic acid-type glutamate receptor is reproducibly associated with response to the antidepressant citalopr...
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rs12762549 and rs11045585 can be used to predict whether docetaxel will induced leukopenia/neutropenia, according to a study of ~100 Japanese patients. When patients were classified into three groups by the scoring system based on the genotypes of these two SNPs, patients with a score of 1 or 2 were shown to have a significantly higher risk of docetaxel-induced leukopenia/neutropenia as compared to those with a score of 0 (P = 0.0000057; odds ratio [OR], 7.00; 95% CI [confidence interval], 2.95-16.59). This prediction system correctly classified 69.2% of severe leukopenia/neutropenia and 75.7% of non-leukopenia/neutropenia into the respective categories. [PharmGKB:Curated In a case control study using samples from BioBank Japan, the G allele of rs12762549 was associated with docetaxel-ind...
depends on [[rs1801252]]
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Also known as Arg389, variation at this SNP, located in the ADRB1 gene, may encode either the amino acid glycine or arginine at amino acid position 389 of the corresponding protein, the beta-1 adrenergic receptor (hence why it is frequently called Arg389Gly). This protein is the target of beta blocker drugs, and so how well the drug works to help lower a patients high blood pressure depends in part on this SNP. The status of this SNP is often reported together with the status of SNP rs1801252, which encodes an amino acid variant at position 49 of the same (ADRB1) protein. The rs1801253(G) allele encodes the glycine. One of the best known studies of the effects of these 2 separate SNPs on the average efficacy of the beta blocker metoprolol in lowering blood pressure (BP) can be summarized f...
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rs2306283 (Asn130Asp/N130D, A388G/388A>G) is a SNP within SLCO1B1 (Solute carrier organic anion transporter family member 1B1). A G at this location denotes the SLCO1B1*1B allele. among 8 healthy volunteers with *1B/*1B genotypes and 16 with the *1A/*1A genotype, *1B/*1B genotype associated with reduced plasma concentrations of repaglinide (but not nateglinide) consistent with increased hepatic uptake by SLCO1B1 (but w/ limited effects on nateglinide pharmacokinetics) news rs2306283 influences statin-related myopathy risk Genotyping panel for assessing response to cancer chemotherapy. Common variants in the SLCO1B3 locus are associated with bilirubin levels and unconjugated hyperbilirubinemia. Pazopanib-induced hyperbilirubinemia is associated with Gilbert's syndrome UGT1A1 polymorphism...
increased risk of cannabis dependence, lower (normal) cancer risk '''Association between ABCB1 C3435T polymorphism and increased risk of cannabis dependence.''' (2009). Patients with cannabis dependence (n=40) had a significantly higher 3435C allele frequency (62.5% versus 43.8% respectively, P=0.017) and CC genotype (50% versus 20%, P=0.005, OR=4.00 [1.50-10.60). The CC genotype was independently associated with cannabis dependence. This is the first time a significant specific genetic marker has been shown in cannabis dependence. ABCB1 polymorphisms may alter Delta9THC distribution, its psychoactive effects and individual vulnerability to dependence.
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rs1045642, also known as C3435T, is a SNP located in the ABCB1 gene. It is often studied in conjunction with rs2032582. C3435T has been mentioned by: * A 'Silent' Polymorphism in the MDR1 Gene Changes Substrate Specificity (for example, to verapamil) * (R)-lansoprazole (Prevacid) concentrations are significantly increased in CYP2C19 extensive metabolizers with ABCB1 C3435T C allele. * In a Korean population, plasma concentrations of fexofenadine (Allegra) were 17% lower in 2677AA/3435CC subjects and 47% higher in the 2677TT/3435TT subjects compared to 2677GG/3435CC subjects. * In contrast, in this study no association was observed between the C3435T polymorphism and fexofenadine plasma or urine concentrations in a German Caucasian population. * A meta-analysis including 9 case-control stud...
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[PharmGKB:Curated This SNP at chromosome 2 is significantly associated with CYP1B1 expression (located on chromosome 2), and daunorubicin IC50 in CEU population using International HapMap cell lines.]
References:6
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Clinically relevant UGT1A10 variant. [PharmGKB:Curated *93 is a common variant of UGT1A1 in Caucasian and African-American populations. It is located in the Phenobarbital Response Enhancer Module (an upstream regulatory sequence) and may be important in predicting irinotecan response.]
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[PharmGKB:Curated The G allele of this SNP is associated with increased incidence of medium-severe nausea or vomiting, and with reduced leukocyte counts in gastric carcinoma and colon carcinoma patients treated with 5-fluorouracil. The elimination constant (Ke) for 5-fluorouracil was significantly lower in patients homozygous for the G allele.]
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rs231775, also known as +49A/G, is a SNP in the CTLA4 gene. which is linked to Hashimoto thyroiditis In a meta-analysis of CTLA4 gene SNPs, rs231775 was most associated with vitiligo; however, the association seems to hold only in the subgroup of patients with other autoimmune diseases. rs231775 (CTLA4_+49_G/A P=0.0219) and rs733618 (CTLA4_-1722_T/C P=0.0096) susceptibility to Graves' disease associated with the development of placental abruption and preeclampsia, with women having the G allele being at risk rs231775 was not associated with type-1 diabetes in a study of 207 Portuguese patients. [PharmGKB:Curated This SNP affects risk for Autoimmune Thyroid Disorder (AITD). The G allele is generally thought to be the risk-conferring allele, but this study found that which allele confers ri...
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[PharmGKB:Curated A study on 50 subjects (25 patients who developed a distinct hearing loss during cisplatin therapy and in 25 patients without hearing impairment after cisplatin therapy)observed a higher frequency of the A-allele of rs2075252 in the LRP2 in the group with hearing impairment than in the group with normal hearing after cisplatin therapy.]
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[PharmGKB:Curated This SNP on chromosome 1 was associated with the susceptibility to daunorubicin-induced cytotoxicity in the YRI population using International HapMap cell lines.]
slower responder
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This SNP in the ACE gene, also known as G12269A, is reported to influence how quickly African Americans respond to the anti-hypertensive drug ramipril. rs4344(A;A) and rs4344(G;G) homozygotes are able to reach lower blood pressure levels upon treatment with ramipril sooner than rs4344(A;G) heterozygotes. The odds ratio reported for this study, comparing both homozygotes to heterozygotes, is 1.86 (CI: 1.32-3.23). Note that this SNP is in almost complete linkage disequilibrium with the insertion/deletion ACE gene SNP.
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[PharmGKB:Curated The G allele of this SNP is part of a haplotype that has been associated with protection from hypersensitivity to carbamazepine.]
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[PharmGKB:Curated Risk or phenotype-associated allele: C. Phenotype: A-444C was associated with aspirin-induced urticaria (AIU). The C allele was more frequent in patients with the cutaneous pattern of AIU and in patients with low skin reactivity to histamine. Study size: 110 patients with AIU and 165 nonallergic controls .]
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[PharmGKB:Curated Risk or phenotype-associated allele: G allele. Phenotype: The G allele of rs1264511 shows strong association with carbamazepine (CBZ)-induced maculopapular exanthema (MPE)/ hypersensitivity syndrome (HSS). Study size: 175. Study population/ethnicity: 31 CBZ-induced MPE/HSS cases and 144 CBZ-tolerant controls of Chinese descent. Significance metric(s): p = 0.001685, OR = 3.13. Type of association: GN; PD; TOX; ADR.]
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[PharmGKB:Curated Risk or phenotype-associated allele: A allele. Phenotype: The A allele rs2894342, which lies in the promoter of MLN, is associated with carbamazepine (CBZ)-induced maculopapular exanthema (MPE)/ hypersensitivity syndrome (HSS). Study size: 175. Study population/ethnicity: 31 CBZ-induced MPE/HSS cases and 144 CBZ-tolerant controls of Chinese descent. Significance metric(s): p = 0.00342, OR = 2.88. Type of association: GN; PD; TOX; ADR.]
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rs20455, often called Arg719 or 719Arg, is a reasonably well studied SNP in the KIF6 gene. The risk allele (encoding the arginine at position 719) is rs20455(C). An extensive 2010 meta-analysis, including over 17,000 patients, suggests this variant does not significantly influence coronary artery disease risk. This SNP is one of the 5 used by Celera's genetic risk score (GRS) for coronary heart disease (CHD). *rs20455, in the KIF6 gene *rs3900940, in the MYH15 gene *rs7439293, in the PALLD gene *rs2298566, in the SNX19 gene *rs1010, in the VAMP8 gene For each of the five variants, the GRS was increased by 1 if the subject was homozygous for the risk variant, unchanged if heterozygous, and decreased by 1 if the individual did not carry the variant. Therefore, individuals carrying all 10 pos...
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[PharmGKB:Curated This variant is in intron 3 of PICK1 and has been significantly associated with methamphetamine abusers in general, and associated with those with spontaneous relapse of psychosis.]
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[PharmGKB:Curated This variant is in intron 4 of PICK1 and has been significantly associated with methamphetamine abusers with spontaneous relapse of psychosis.]
normal risk
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rs7997012, located in an intron of the HTR2A gene, was found to be associated with a somewhat increased rate of successful response to treatment of depression with the drug citalopram. From this article : 'HTR2A encodes the serotonin 2A receptor, which is downregulated by citalopram. Participants who were homozygous for the A allele had an 18% reduction in absolute risk of having no response to treatment, compared with those homozygous for the other allele.' * See also Anxiety Blog posting [PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: Patients with the 5-HTR2A intron 2 (rs7997012) AA genotype suffered from more pronounced side effects compared to carriers of the GA or GG genotype. Study size: 124. Study population/ethnicity: Caucasian; Patients with psychiatric diso...
common in clinvar
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Technology to accelerate pangenomic scanning for unknown point mutations in exonic sequences: cycling temperature capillary electrophoresis (CTCE). Genetic variation in the one-carbon transfer pathway and ovarian cancer risk. Strong association of a common dihydropyrimidine dehydrogenase gene polymorphism with fluoropyrimidine-related toxicity in cancer patients. Genetic variation in TYMS in the one-carbon transfer pathway is associated with ovarian carcinoma types in the Ovarian Cancer Association Consortium. [PharmGKB:Curated Patients heterozygous for the C allele of this SNP exhibited increased incidence of medium-severe nausea and vomiting (as defined by WHO criteria) relative to those carrying only the T allele. The patient population consisted of individuals with gastric or colon ca...
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rs2227956 in HSP70-hom, resulted in a significant association with noise-induced hearing loss [PharmGKB:Curated The C allele of this SNP is part of a haplotype that has been associated with protection from hypersensitivity to carbamazepine.] [OMIM:?]
normal
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This SNP, located in an intron of the GRIA3 gene (also known as AMPA3), has been linked in one study to increased thoughts of suicide in patients taking the anti-depressant drug citalopram. The increased risk is calculated to be 1.9x. If the individual is also carrying two rs2518224(C) alleles, i.e. is a rs2518224(C;C) homozygote, the odds ratio for having suicidal thoughts is increased to ~15x (CI: 3.7 - 60.6). [PharmGKB:Curated This SNP in the GRIA3 gene was associated with treatment-emergent suicidal ideation during citalopram therapy in a clinically representative cohort of outpatients with major depressive disorder. DNA samples from 1,915 participants were genotyped.]
27 snps
(hide) Endurance
Mix of muscle types. Likely sprinter. Normal for white people. One working and one defective copy of the gene for alpha-actinin-3 in fast-twitch muscle fibres. This genotype may indicate somewhat impaired muscles, however many sprinters and some endurance athletes have this.
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This SNP, in the ACTN3 gene, encodes a premature stop codon in a muscle protein called alpha-actinin-3. The polymorphism alters position 577 of the alpha-actinin-3 protein. In the (C;C) genotype is often called RR. The truncated (T;T) is often called XX. (T;T) is under-represented in elite strength athletes, consistent with previous reports indicating that alpha-actinin-3 deficiency appears to impair muscle performance. The most common nucleotide at this position, (C), encodes an arginine (amino acid code R), the alternative T allele encodes a stop codon (X). Hence, the SNP is referred to as R577X, with homozygotes being either RR or XX and heterozygotes being RX. XX individuals completely lack the expression of alpha-actinin-3. An earlier report studying a relatively small number of Austr...
1.3x increased risk that pediatric inhaler use may make asthma worse
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rs1042713, also known as Arg16, G16R, and 16Arg>Gly, is a SNP in the adrenergic, beta-2-, surface receptor ADRB2 gene. The rs1042713(G) allele encodes the G/glycine form that is the more common one in most populations, while rs1042713(A) encodes the R/arginine residue at this position of the ADRB2 protein. A study of 1,182 young Scottish asthma patients (age, 3-22 years) concluded that rs1042713(A) alleles are significantly associated with 'exacerbations' of their condition, regardless of treatment regimens (odds ratio 1.30, CI: 1.09-1.55, p=0.003). This didn't hold true for patients using inhalers less than once per day; and it was particularly true for those receiving daily inhaled long- or short-acting beta(2)-agonist treatment (OR, 1.64, CI: 1.22-2.20, p=.001). This may therefore in...
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In 'Association of the ADRA2A polymorphisms with the risk of type 2 diabetes: a meta-analysis.' a meta-analysis of publications prior to September 2012 showed no overall association between rs553668 and T2D risk, but did find an association with very high (poor) P-value for Europeans under recessive gene model (GT=AA, OR=1.36, p=0.02, 95% CI: 1.05, 1.76). In 'Genetic association of adrenergic receptor alpha 2A with obesity and type 2 diabetes.' rs553668 was found to correlate with obesity in Swedish population, but not significantly for BMI-corrected T2D risk. ADRA2A is involved in sympathetic nervous system's inhibition of insulin secretion and lipolysis, so direct effect on T2D is usually sought, but the Swedish study suggest it could work through body mass. It also mentions that rs55366...
depends on [[rs1801252]]
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Also known as Arg389, variation at this SNP, located in the ADRB1 gene, may encode either the amino acid glycine or arginine at amino acid position 389 of the corresponding protein, the beta-1 adrenergic receptor (hence why it is frequently called Arg389Gly). This protein is the target of beta blocker drugs, and so how well the drug works to help lower a patients high blood pressure depends in part on this SNP. The status of this SNP is often reported together with the status of SNP rs1801252, which encodes an amino acid variant at position 49 of the same (ADRB1) protein. The rs1801253(G) allele encodes the glycine. One of the best known studies of the effects of these 2 separate SNPs on the average efficacy of the beta blocker metoprolol in lowering blood pressure (BP) can be summarized f...
References:5
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[PharmGKB:Curated The -58C allele of the human beta2 bradykinin receptor gene has been associated with hypertension in a Chinese Han population and an African American population.]
complex; see details for increased risks
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Several susceptibilities have been linked to rs1042714, a SNP in the ADRB2 gene that is also known as the Q27E SNP. The rs1042714(C) allele encodes the glutamine (Gln; 'Q'), and the rs1042714(G) allele encodes the glutamic acid (Glu; 'E'). A study of 304 patients found that the Glu27 allele led to increased risk for idiopathic venous thromboembolism; the reported odds ratio was 1.40 (CI: 1.09-1.79, p=0.006) for carriers of at least one risk allele. A study of 334 families with at least one child with autism found that increased risk associated with the rs1042714(G;G) homozygous genotype; the odds ratio reported was between 1.33-1.60 (CI: 1.07-2.58). The risk was approximately doubled among mothers who had clinical markers for pregnancy related stress. In a study of 342 patients with type-2...
7 snps
(hide) Eye color
Magnitude: 2.5
Blue eyes
thumb Heterozygous for what calls blue eye color haplotype #1. It seems 'blue', might be overstating it. In the eye color research community, there seems to be a distinction between the dark brown eyes typical for asian and african ancestry, and 'blue' for lighter eyes found in europeans.
Generally European; Light skin; Possibly an increased risk of melanoma This SNP is associated with skin, hair, and eye colour, and risk of melanoma. Individuals with the G;G genotype are generally of European descent and have fair skin. In a population-based case-control study investigating a number of pigmentation-related SNPs and their correlation with cutaneous malignant melanoma (CMM) in a Caucasian Australian population, rs16891982 (variant F374L) was found to be associated with odds ratios of 3.44, 2.86, 1.68, and 1.68 for all study subjects (1,738 CMM cases and 4,517 controls); subjects with northern European ancestry (1,438 cases and 3,098 controls); northern European subjects adjusted for hair, eye, and skin colour; and northern European subjects adjusted for the MC1R genotype, r...
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This snp influences skin pigmentation. The allele p.L374F indicates light-skinned european ancestry c.1122C>G, p.Phe374Leu (NCBI dbSNP rs16891982) in SLC45A2 was associated with protection from malignant melanoma (OR, 0.41; 95% CI, 0.24-0.70; P=0.008 after adjustment for multiple testing) An association study conducted on a population of European origin concluded that the rare (in Europeans, at least) allele L374, i.e. rs16891982(C) in dbSNP orientation, significantly increases the possibility of having black hair color, with an odds ratio of around 7. This population-based case-control study investigated a number of pigmentation-related SNPs and their correlation with cutaneous malignant melanoma (CMM) in an Australian population. rs16891982 (variant F374L) was found to be associated w...
Frequency: 47.8%
References:0
References:0
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Influences appearance gnxp
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Influences appearance gnxp [OMIM:AGOUTI SIGNALING PROTEIN; ASIP]
Frequency: 26.2%
References:1
References:1
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[GWAS:None]
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Influences appearance gnxp A genomewide association study of skin pigmentation in a South Asian population. Complex signatures of selection for the melanogenic loci TYR, TYRP1 and DCT in humans.
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[GWAS:Eye color]
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[GWAS:None]
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freckling [OMIM:OCA2 GENE]
usually brown eye color
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rs4778241 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozygous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C)<br> rs1129038(A)<br> rs12593929(A)<br> rs12913832(G)<br> rs7183877(C)<br> rs3935591(G)<br> rs7170852(A)<br> rs2238289(T)<br> rs3940272(C)<br> rs8028689(T)<br> rs2240203(A)<br> rs11631797(G)<br> rs916977(G)<br> A three-single-nucleotide polymorphism haplotype in intron 1 of OCA2 explains most human eye-color variatio...
blue/gray eyes less likely
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rs7495174 is located in intron 1 of the OCA2 gene. The (A) allele (in dbSNP orientation) is associated with blue or green eye color in Caucasians. . This SNP is 1 of 3 SNPs defining a haplotype that has been studied for association with eye color. The full details on the correspondence between the haplotype and eye color can be found on the OCA2 page. [PharmGKB:Curated A haplotype containing rs11855019, rs6497268 and rs7495174 was highly associated with eye color, hair color and skin pigmentation in a mostly Northern European twin study.] [OMIM:OCA2 GENE]
brown eye color
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rs1129038 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozygous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C)<br> rs1129038(A)<br> rs12593929(A)<br> rs12913832(G)<br> rs7183877(C)<br> rs3935591(G)<br> rs7170852(A)<br> rs2238289(T)<br> rs3940272(C)<br> rs8028689(T)<br> rs2240203(A)<br> rs11631797(G)<br> rs916977(G)<br> [OMIM:HECT DOMAIN AND RCC1-LIKE DOMAIN 2; HERC2] [GWAS:None]
Frequency: 34.5%
References:32
References:32
brown eye color
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rs12913832 is a SNP near the OCA2 gene that may be functionally linked to blue or brown eye color, due to a lowering of promoter activity of the OCA2 gene. Blue eye color is associated with the rs12913832(G;G) genotype. For green versus blue eye color rs12913832 in OCA2/HERC2 has a score of 51.5 and an estimated allelic OR of 8.43 . The SNP rs1667394 in this same region has an estimated OR of (4.85–10.06). rs12913832 is also part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, that is found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other racial groups. rs12913832-T (brown eye) homozygotes compared to rs12913832-C (blue eye). correlations with...
usually brown eye color
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rs7183877 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozygous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C)<br> rs1129038(A)<br> rs12593929(A)<br> rs12913832(G)<br> rs7183877(C)<br> rs3935591(G)<br> rs7170852(A)<br> rs2238289(T)<br> rs3940272(C)<br> rs8028689(T)<br> rs2240203(A)<br> rs11631797(G)<br> rs916977(G)<br>
usually brown eye color
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rs3935591 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozygous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C) rs1129038(A) rs12593929(A) rs12913832(G) rs7183877(C) rs3935591(G) rs7170852(A) rs2238289(T) rs3940272(C) rs8028689(T) rs2240203(A) rs11631797(G) rs916977(G)
usually brown eye color
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rs7170852 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozygous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C)<br> rs1129038(A)<br> rs12593929(A)<br> rs12913832(G)<br> rs7183877(C)<br> rs3935591(G)<br> rs7170852(A)<br> rs2238289(T)<br> rs3940272(C)<br> rs8028689(T)<br> rs2240203(A)<br> rs11631797(G)<br> rs916977(G)<br>
usually brown eye color
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rs2238289 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozygous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C)<br> rs1129038(A)<br> rs12593929(A)<br> rs12913832(G)<br> rs7183877(C)<br> rs3935591(G)<br> rs7170852(A)<br> rs2238289(T)<br> rs3940272(C)<br> rs8028689(T)<br> rs2240203(A)<br> rs11631797(G)<br> rs916977(G)<br> Genetic determinants of hair and eye colours in the Scottish and Danish populations.
usually brown eye color
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rs3940272 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozygous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C)<br> rs1129038(A)<br> rs12593929(A)<br> rs12913832(G)<br> rs7183877(C)<br> rs3935591(G)<br> rs7170852(A)<br> rs2238289(T)<br> rs3940272(C)<br> rs8028689(T)<br> rs2240203(A)<br> rs11631797(G)<br> rs916977(G)<br>
Frequency: 23.1%
References:1
References:1
usually brown eye color
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rs11631797 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozygous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C)<br> rs1129038(A)<br> rs12593929(A)<br> rs12913832(G)<br> rs7183877(C)<br> rs3935591(G)<br> rs7170852(A)<br> rs2238289(T)<br> rs3940272(C)<br> rs8028689(T)<br> rs2240203(A)<br> rs11631797(G)<br> rs916977(G)<br>
brown eye color is more likely
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rs916977 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozygous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C)<br> rs1129038(A)<br> rs12593929(A)<br> rs12913832(G)<br> rs7183877(C)<br> rs3935591(G)<br> rs7170852(A)<br> rs2238289(T)<br> rs3940272(C)<br> rs8028689(T)<br> rs2240203(A)<br> rs11631797(G)<br> rs916977(G)<br> [PharmGKB:Non-Curated GWAS results: Three genome-wide association studies and a linkage analysis identify H...
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rs1667394 increases susceptibility to Blond rather than brown hair 4.94 times for carriers of the A allele rs1667394 increases susceptibility to Blue rather than brown eyes 29.43 times for carriers of the A allele rs1667394 increases susceptibility to Blue rather than green eyes 6.74 times for carriers of the A allele For green versus blue eye color rs12913832 in OCA2/HERC2 has a score of 51.5 and an estimated allelic OR of 8.43 . The SNP rs1667394 in this same region has an estimated OR of (4.85–10.06). [OMIM:HECT DOMAIN AND RCC1-LIKE DOMAIN 2; HERC2] [GWAS:Eye color]
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[GWAS:Eye color traits]
References:1
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[GWAS:Eye color]
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[GWAS:Eye color]
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[GWAS:Eye color traits]
normal
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rs4911414 is a SNP near the ASIP (agouti signaling protein) gene on chromosome 20. This SNP is one of a tightly-linked pair that increases the likelihood of an individual being prone to sun sensitivity, in other words, freckles and sunburn, based on a study of 6,000+ Caucasians (5,000+ Icelanders + 1,000+ Dutch). The odds ratios, presumably on a dominant basis, and at least in the largest population (Icelanders) for 'freckles and burns vs. no freckles and tans' for the haplotype pair rs1015362(G) - rs4911414(T) is 3.91 (CI: 2.54-6.03) for males and 2.42 (CI: 1.52-3.86) for females, with an overall p=0.051. Based on a study by the same authors of 4,000+ skin cancer patients, this haplotype was seen to confer significant increased risk for cutaneous malignant melanoma (odds ratio 1.45, p = 1...
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Influences appearance gnxp Digital Quantification of Human Eye Color Highlights Genetic Association of Three New Loci[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865509/] Common sequence variants on 20q11.22 confer melanoma susceptibility. Genome-wide association study identifies three loci associated with melanoma risk. Web-based, participant-driven studies yield novel genetic associations for common traits.
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[PharmGKB:Non-Curated GWAS Results: Two newly identified genetic determinants of pigmentation in Europeans (Initial Sample Size: 5,130 individuals; Replication Sample Size: 3,330 individuals; Risk/trait Allele: rs1408799-C). This variant is associated with Blue vs. green eyes.] [OMIM:TYROSINASE-RELATED PROTEIN 1; TYRP1] [GWAS:Eye color] [GWAS:Blue vs. green eyes]
Magnitude: 0
Frequency: 88.5%
Repute:Good
References:1
Frequency: 88.5%
Repute:Good
References:1
blue eye color more likely
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rs12593929 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozgyous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C)<br> rs1129038(A)<br> rs12593929(A)<br> rs12913832(G)<br> rs7183877(C)<br> rs3935591(G)<br> rs7170852(A)<br> rs2238289(T)<br> rs3940272(C)<br> rs8028689(T)<br> rs2240203(A)<br> rs11631797(G)<br> rs916977(G)<br>
1 genoset 30 snps
(hide) Family Tree DNA Factoids
2x increased risk of Male Pattern Baldness. Verified in Europeans and Asians. Family Tree DNA reports this SNP as more likely to go bald, but 23andMe doesn't mention it.
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spitoon rs2180439(T;T) have 2x increased odds of male pattern baldness. [PharmGKB:Non-Curated Susceptibility variants for male-pattern baldness on chromosome 20p11. (Initial Sample Size: 296 cases, 347 controls; Replication Sample Size: 319 cases, 234 controls); (Region: 20p11.22; Reported Gene: PAX1, BQ013595, BE789145; Risk Allele: rs2180439-C) This variant is associated with Male-pattern baldness.] [OMIM:ALOPECIA, ANDROGENETIC, 3; AGA3] [GWAS:Male-pattern baldness]
A1/A2: Bad at avoidance of errors. 0.5x lower OCD risk, 0.87x lower Tardive Diskinesia risk, higher ADHD risk. More Alcohol Dependence. Lower risk of Postoperative Nausea. Increased obesity. Bupropion is not effective. The DRD2 TaqIA A1/A2 version causes less dopamine receptors. Doesn't learn from mistakes well. Reduced response to errors and increased addictive behavior Men may have half the risk of Obsessive Compulsive Disorder but higher risk of ADHD. Women have lower Persistence. 0.87x reduced risk of Tardive Diskinesia when taking dopamine receptor antagonists. Slightly increased risk of alcoholism and smoking addiction. Slower recovery from traumatic brain injury. Lower risk of postoperative nausea within 6 hours of surgery. Bupropion (Wellbutrin, Budeprion, Prexaton, Elontril, Aple...
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rs1800497, a SNP also known as the TaqIA (or Taq1A) polymorphism of the dopamine D2 receptor DRD2 gene (even though it is actually located over 10,000bp downstream of the gene), gives rise to the DRD2*A1 allele. This allele (rs1800497(T)) is associated with a reduced number of dopamine binding sites in the brain . Reduced response to errors and increased addictive behavior It has been postulated to play a role in alcoholism, smoking, and certain neuropsychiatric disorders. The reduced number of dopamine binding sites may play a role in nicotine addiction by causing an 'understimulated' state that can be relieved by smoking (and/or use of other drugs). A wide variety of reports have been published over more than ten years either linking rs1800497 to aspects of nicotine use and smoking cessa...
Mix of muscle types. Likely sprinter. Normal for white people. One working and one defective copy of the gene for alpha-actinin-3 in fast-twitch muscle fibres. This genotype may indicate somewhat impaired muscles, however many sprinters and some endurance athletes have this.
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This SNP, in the ACTN3 gene, encodes a premature stop codon in a muscle protein called alpha-actinin-3. The polymorphism alters position 577 of the alpha-actinin-3 protein. In the (C;C) genotype is often called RR. The truncated (T;T) is often called XX. (T;T) is under-represented in elite strength athletes, consistent with previous reports indicating that alpha-actinin-3 deficiency appears to impair muscle performance. The most common nucleotide at this position, (C), encodes an arginine (amino acid code R), the alternative T allele encodes a stop codon (X). Hence, the SNP is referred to as R577X, with homozygotes being either RR or XX and heterozygotes being RX. XX individuals completely lack the expression of alpha-actinin-3. An earlier report studying a relatively small number of Austr...
Carrier of one CYP1A2*1F allele; Slow Caffeine Metabolizer. One copy of the slow caffeine metaboliser SNP, and one copy of the fast version. This makes you more strongly affected by drinking coffee, as caffeine is broken down slower in the liver. Supposedly this increases the risk of heart attacks, although other studies show caffeine is generally good for the heart. It also makes caffeine more effective at preventing Breast Cancer, Alzheimer's Disease, and Parkinson's disease. Too much caffeine will shrink your breasts.
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rs762551, also known as -164A>C or -163C>A, is a SNP encoding the CYP1A2*1F allele of the CYP1A2 gene. For historic reasons, the rs762551(C) allele is considered the wild-type, even though it is the rarer allele in most populations. The rs762551(A) allele is the 'fast metabolizer' allele known as CYP1A2*1F; the (C) allele is by comparison a slower metabolizer of certain substrates (including caffeine). In terms of genotypes, only rs762551(A;A) individuals are considered fast metabolizers. Individuals who are rs762551(A;C) heterozygotes or rs762551(C;C) homozygotes are both considered slow metabolizers. The CYP1A2 gene encodes a member of the cytochrome p450 family of proteins, which metabolize nutrients and drugs. One well known substrate of CYP1A2 is caffeine; individuals who are ca...
Normal (worse) aging. This is the less beneficial version of the SIRT1 longevity gene, which doesn't extend lifespan. It is normal in non-Asians. It has more cognitive decline with age. Taking resveratrol is also believed to increase longevity via the SIRT1 gene, so it might (or might not) be possible to mitigate this with resveratrol supplements or some other SIRT1 activator.
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rs3758391, a SNP in the SIRT1 gene, has been reported to potentially have some role in either longevity, or with higher statistical significance, better cognitive function in older individuals. SIRT1 is thought to regulate neuronal metabolism and survival in response to stress, and the equivalent gene in other species influences maximal life span. The study reporting improved cognition for carriers of rs3758391(T) alleles was based on over 1,000 Finnish adults over the age of 85, and a weak trend towards lower cardiovascular disease was also reported for this allele.
Normal (higher) risk of physical impairment with age. This causes physical problems for older people, and Cerebral Small Vessel Disease in the brain.
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rs2811712 is a SNP associated with physical function in older individuals, and thus indirectly associated with longevity. In a study ultimately totaling over 3,300 elderly Caucasian individuals, the less common rs2811712(G) allele was associated with reduced physical impairment. Overall, severely limited physical function was present in 15.0% of the more common rs2811712(A;A) homozygotes, versus 7.0% of the rs2811712(G;G) homozygotes, yielding a per risk allele odds ratio of 1.48 (CI: 1.17-1.88, p=0.001). Association of single-nucleotide polymorphisms in the cell cycle genes with breast cancer in the British population. Consortium analysis of 7 candidate SNPs for ovarian cancer. Candidate gene analysis using imputed genotypes: cell cycle single-nucleotide polymorphisms and ovarian cancer r...
Back Pain: lower risk of Lumbar Disc Disease. This appears to reduce the risk of LDD, at least in Japanese people and women.
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The rs2073711 SNP (1184T→C ) is located in exon 8 of the cartilage intermediate layer protein gene (CILP). However, CILP gene is primarily known to be expressed abundantly in intervertebral discs, and was reported to have increased expression when degeneration occurs . For the rs2073711 SNP, the ancestral allele is T and the disease associated risk allele is C. A study of Asian patients with lumbar disc disease (LDD) implicates each copy of a (C) allele of SNP rs2073711 (as oriented with respect to dbSNP) as increasing risk about 1.6 fold. ==Background== Low back pain (LBP) is an enervating condition that affects 70-85% of all people during their lifetime . It can lead to decreased physical activity and quality of life, presenting considerable negative socioeconomic and health impact...
Lower risk of dementia and Alzheimer's disease. Higher good cholesterol. One copy of a longevity gene. This seems to raise HDL ('good') cholesterol, and reduce the risk of dementia and Alzheimer's disease. It may slightly increase longevity. It has been particularly studied in Ashkenazi Jews.
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This SNP rs5882 in the CETP gene referred to as ILE405VAL and RSAI405V has been related to ageing and exceptional long life. A study in Ashkenazi Jews showed that individuals homozygotic for the G allele have significantly longer lifespans. New research also indicates that G homozygotes have an average of 70% less risk of dementia and Alzheimer's disease. The study also found that heterozygotes have a lower risk of dementia and Alzheimer's disease but more study is needed to determine the risk reduction for heterozygotes. See Association of a Functional Polymorphism in the Cholesteryl Ester Transfer Protein (CETP) Gene With Memory Decline and Incidence of Dementia and CETP Variant Linked to Slower Cognitive Decline and Reduced Dementia Risk . [PharmGKB:Curated Risk or phenotype-associated...
Common variant. Slightly shorter lifespan. Chemotherapy is less effective. Accelerated lung decline in smokers. African Americans have 2.15x risk of dying from colo-rectal cancer.
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This SNP, a variant in the TP53 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the G allele encodes an arginine at position 72 of the protein (where there's normally a proline), and the SNP is commonly called the Arg72 variant, although P72R and Arg72Pro are also common in the literature. Minor allele homozygotes, i.e. rs1042522(C;C) genotypes, live on average 3 years longer than major allele (G;G) homozygotes, based on a study of 9,200+ Danish individuals. The increased longevity is speculated to be related to the i...
Can taste bitter. Normal tasting ability for bitterness. This makes turnip, cabbage, brussels sprouts, broccoli, and other cruciferous vegetables taste more interesting and less horribly bland. Coffee and dark beers also tastes more bitter. You can taste propylthiouracil (PROP), PTC, and related chemicals. On the other hand, you can't taste the unpleasant bitterness of the tropical fruit from the Bignay tree, it will taste sweet to you. You probably eat healthier.
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rs713598 is one of three SNPs that form the main haplotypes behind the ability to perceive as bitter the taste of the compound phenylthiocarbamide (PTC) and similar molecules in foods (like cabbage and raw broccoli) or drinks (like coffee and dark beers). The rs713598(G) allele, in the orientation shown in dbSNP, is the 'tasting' allele, and it is dominant to the 'non-tasting' allele rs713598(C), so having one copy is enough to have the bitter tasting ability. If you are a 'taster', you're also likely to carry at least one rs10246939(C) and one rs1726866(C) allele since, along with rs713598(G), these three SNPs form the most common tasting haplotype. If you lack these alleles, you're quite likely (~80%) to be a non-taster of bitterness, meaning that foods that may taste bitter to others ta...
complex; see details
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rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. Studies on rs1800795 now include potential associations with heart disease, Kaposi's sarcoma, type-2 diabetes, stroke, obesity, Hodgkin's lymphoma, sudden ...
Magnitude: 0.1
References:10
References:10
can taste bitter
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rs10246939 is one of three SNPs that form the main haplotypes behind the ability to perceive as bitter the taste of the compound phenylthiocarbamide (PTC) and similar molecules in foods (like cabbage and raw broccoli) or drinks (like coffee and dark beers). The rs10246939(C) allele, in the orientation shown in dbSNP, is the 'tasting' allele, and it is dominant to the 'non-tasting' allele rs10246939(T), so having one copy is enough to have the bitter tasting ability. If you are a 'taster', you're also likely to carry at least one rs713598(G) and one rs1726866(C) allele since, along with rs10246939(C), these three SNPs form the most common tasting haplotype. If you lack these alleles, you're quite likely (~80%) to be a non-taster of bitterness, meaning that foods that may taste bitter to oth...
can taste bitter
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rs1726866 is one of three SNPs that form the main haplotypes behind the ability to perceive as bitter the taste of the compound phenylthiocarbamide (PTC) and similar molecules in foods (like cabbage and raw broccoli) or drinks (like coffee and dark beers). The rs1726866(C) allele is the 'tasting' allele, and it is dominant to the 'non-tasting' allele rs1726866(T), so having one copy is enough to have the bitter tasting ability. If you are a 'taster', you're also likely to carry at least one rs713598(G) and one rs10246939(C) allele since, along with rs1726866(C), these three SNPs form the most common tasting haplotype. If you lack these alleles, you're quite likely (~80%) to be a non-taster of bitterness, meaning that foods that may taste bitter to others taste far less bitter to you. (C;C)...
normal
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rs4911414 is a SNP near the ASIP (agouti signaling protein) gene on chromosome 20. This SNP is one of a tightly-linked pair that increases the likelihood of an individual being prone to sun sensitivity, in other words, freckles and sunburn, based on a study of 6,000+ Caucasians (5,000+ Icelanders + 1,000+ Dutch). The odds ratios, presumably on a dominant basis, and at least in the largest population (Icelanders) for 'freckles and burns vs. no freckles and tans' for the haplotype pair rs1015362(G) - rs4911414(T) is 3.91 (CI: 2.54-6.03) for males and 2.42 (CI: 1.52-3.86) for females, with an overall p=0.051. Based on a study by the same authors of 4,000+ skin cancer patients, this haplotype was seen to confer significant increased risk for cutaneous malignant melanoma (odds ratio 1.45, p = 1...
14 snps
(hide) Folate
homozygous for C677T of MTHFR = 10-20% efficiency in processing folic acid = high homocysteine, low B12 and folate levels This is the homozygous form of the C677T allele for the MTHFR gene. It is found in approximately * 15% of Hispanic Americans * 12% of Caucasian Americans * 12% of Japanese * 6% of Germans * 3% of Asians * 2% of African Americans * 1% of Sub-Saharan Africans Numerous health effects are associated with this variant. * Hyperhomocysteinemia and neurologic disorders: a review. (2014). A review. Certain genetic factors also cause elevated homocysteine levels, such as C667T substitution of the gene encoding methylenetetrahydrofolate reductase. Elevated homocysteine has been observed in several medical conditions, such as cardiovascular disorders, atherosclerosis, myocardial i...
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer ** renal cancer * cleft lip and cleft palate * coronary artery disease * dementia * depression * hyperhomocysteinemia * migraine * neural tube d...
1.45 ng/mL lower Vitamin B6 blood concentration
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This is one of the SNPs reported by NutraHacker. Genetics and genomics of human aging. [PharmGKB:Non-Curated The C allele of this SNP is associated with lower blood concentration of vitamin B6 (Combined studies of Tuscan Italians ( inCHIANTI:N =1175 and Progetto Nutrizione study:N = 687) found 1.45 ng/mL lower vitamin B6 per copy of C (p = 8.3 x 10 (-18)))] [OMIM:?] [GWAS:Folate pathway vitamins]
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[PharmGKB:Non-Curated GWAS results: Genome-wide Association Study of Vitamin B6, Vitamin B12, Folate, and Homocysteine Blood Concentrations. (Initial Sample Size: 2,934 individuals; Replication Sample Size: 686 individuals); (Region: 3p14.1; Reported Gene(s): PRICKLE2; Risk Allele: rs153734-T); (p-value= 0.000007).This variant is associated with Folate pathway vitamins.] [GWAS:Folate pathway vitamins]
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rs1076991 C > T exerts a significant effect on promoter activity in vitro and along with rs2236225 G > A influences embryonic development. Common genetic polymorphisms affect the human requirement for the nutrient choline. Neural tube defects and folate pathway genes: family-based association tests of gene-gene and gene-environment interactions. Gene response elements, genetic polymorphisms and epigenetics influence the human dietary requirement for choline. Lymphocyte gene expression in subjects fed a low-choline diet differs between those who develop organ dysfunction and those who do not. Folate and one-carbon metabolism gene polymorphisms and their associations with oral facial clefts. Association of polymorphisms in one-carbon metabolizing genes and lung cancer risk: a case-cont...
4 snps
(hide) Forensically Useful Morphological Traits
None
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Influences appearance The A allele of rs1042602 is associated with the absence of freckles [PharmGKB:Non-Curated GWAS Results: A genomewide association study of skin pigmentation in a South Asian population (Initial Sample Size: 363 with maxL* < 56 and 374 with maxL* > 63; 20% tails of distribution; Replication Sample Size: 116 low maxL*, 115 high maxL* individuals). This variant is associated with skin pigmentation by reflectance spectroscopy.] [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 3; SHEP3] [GWAS:Freckles] [GWAS:Skin pigmentation by reflectance spectroscopy]
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Influences appearance gnxp A genomewide association study of skin pigmentation in a South Asian population. Complex signatures of selection for the melanogenic loci TYR, TYRP1 and DCT in humans.
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rs1805005, known as Val60Leu or V60L, is a SNP in the MC1R gene associated with light blond hair color in one study. The risk allele is rs1805005(T), compared with the wild-type rs1805005(G) allele. See also OMIM 155555.0006 [OMIM:?]
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news three SNPs that appear to have different effects in men and women rs3846662 rs2304130 rs2083637 journal LDL-Cholesterol minor allele was associated with up to 2.2-fold lower expression Common SNPs in HMGCR in micronesians and whites associated with LDL-cholesterol levels affect alternative splicing of exon13. The HMG-CoA reductase gene and lipid and lipoprotein levels: the multi-ethnic study of atherosclerosis. Genetic loci associated with plasma concentration of low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, triglycerides, apolipoprotein A1, and Apolipoprotein B among 6382 white women in genome-wide analysis with replication. Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip. Analysis of recently identifie...
common in complete genomics
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A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. [GWAS:Tanning]
7 snps
(hide) Freckling
None
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Influences appearance The A allele of rs1042602 is associated with the absence of freckles [PharmGKB:Non-Curated GWAS Results: A genomewide association study of skin pigmentation in a South Asian population (Initial Sample Size: 363 with maxL* < 56 and 374 with maxL* > 63; 20% tails of distribution; Replication Sample Size: 116 low maxL*, 115 high maxL* individuals). This variant is associated with skin pigmentation by reflectance spectroscopy.] [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 3; SHEP3] [GWAS:Freckles] [GWAS:Skin pigmentation by reflectance spectroscopy]
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An association between freckling and rs2153271 [GWAS:Freckling]
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freckling [OMIM:OCA2 GENE]
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plos the association between rs12203592 and hair color was independent of rs1540771, a SNP between the IRF4 and EXOC2 genes previously found to be associated with hair color. [PharmGKB:Non-Curated GWAS Results: Genetic determinants of hair, eye and skin pigmentation in Europeans (Initial Sample Size: 2,986 individuals; Replication Sample Size: 3,932 individuals). This variant is associated with freckles.] [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 8; SHEP8] [GWAS:Freckles]
5 snps
(hide) French-Canadian
possibly lower HDL cholesterol in women One report indicates that women (but not men) with this genotype may have slightly lower levels of HDL cholesterol, but other reports have not observed this.
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rs5370, also known as Lys198Asn or K198N, is a SNP in the endothelin-1 EDN1 gene on chromosome 6. The generally more common rs5370(G) allele encodes the Lys (K), and the rarer rs5370(T) allele encodes the Asn (N). Among the French-Canadian founder population of the Saguenay Lac St-Jean region of Quebec, rs5370(T) was associated with lower HDL cholesterol values in women (p = 1.3 x 10e-5), but not in men. In a study of 1,000+ Western Australians, no association was seen between HDL levels and rs5370. A study of ~400 rheumatoid arthritis patients found a 3x increase in the adjusted odds of being hypertensive for rs5370(T;T) homozygotes compared to (G;G) homozygotes (odds ratio 2.89, CI: 1.02 - 8.19, p=0.011). After adjustment for multiple potential confounders, haplotype analysis revealed an...
1.9x risk for pre-eclampsia
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rs4762, a SNP in the angiotensin II AGT gene, has been reported to be associated with increased risk for developing pre-eclampsia, based on a study of ~180 French-Canadian women. The odds ratio associated with the rs4762(T) allele (encoding methionine) was 1.9 (CI:1.2–2.9, p=0.0033). Note that rs4762 is commonly referred to in the literature as 'T174M' or 'Thr174Met'; however, databases now indicate that the amino acid that varies is #207 (not 174), as the protein is currently numbered. rs4762 was also reported to play the major role in the 2.1 fold increased risk (CI: 1.4-3.4, p=0.0008) for pre-eclampsia of the rs3889728(A)-rs4762(T)-rs699(C) haplotype. Correction of population stratification in large multi-ethnic association studies. Ten renin-angiotensin system-relate...
2 snps
(hide) GCH1
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Polymorphic Variation of the Guanosine Triphosphate Cyclohydrolase 1 Gene Predicts Outcome in Patients Undergoing Surgical Treatment for Lumbar Degenerative Disc Disease Lack of influence of GTP cyclohydrolase gene (GCH1) variations on pain sensitivity in humans. Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project.
References:1
References:0
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Polymorphic Variation of the COMT and GCH1 Genes In Patients Undergoing Surgical Treatment For Lumbar Degenerative Disc Disease Lack of influence of GTP cyclohydrolase gene (GCH1) variations on pain sensitivity in humans.
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[GWAS:None]
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A GCH1 Haplotype Associated with Susceptibility to Vasoocclusive Pain and Impaired Vascular Function in Sickle Cell Anemia
6 snps
(hide) GeneTest SNPs on Arrays
homozygous for C677T of MTHFR = 10-20% efficiency in processing folic acid = high homocysteine, low B12 and folate levels This is the homozygous form of the C677T allele for the MTHFR gene. It is found in approximately * 15% of Hispanic Americans * 12% of Caucasian Americans * 12% of Japanese * 6% of Germans * 3% of Asians * 2% of African Americans * 1% of Sub-Saharan Africans Numerous health effects are associated with this variant. * Hyperhomocysteinemia and neurologic disorders: a review. (2014). A review. Certain genetic factors also cause elevated homocysteine levels, such as C667T substitution of the gene encoding methylenetetrahydrofolate reductase. Elevated homocysteine has been observed in several medical conditions, such as cardiovascular disorders, atherosclerosis, myocardial i...
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer ** renal cancer * cleft lip and cleft palate * coronary artery disease * dementia * depression * hyperhomocysteinemia * migraine * neural tube d...
One copy of H63D, carrier of hemochromatosis, likely unaffected unless also C282Y carrier. You are a carrier for rs1799945(G) H63D Hereditary hemochromatosis. You are unlikely to be affected unless also a carrier of rs1800562(A) C282Y, but others in your family may be. This is a treatable condition.
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rs1799945, also known as H63D or His63Asp, represents a SNP that accounts for a mild form of hereditary hemochromatosis (HH), an iron overload condition in which mutations of certain genes involved in iron metabolism disrupt the body’s ability to regulate uptake of iron, causing increased intestinal iron absorption. The most common form is caused by mutations in the HFE gene, which are inherited recessively. The gene for HH is closely linked to the HLA-A3 locus on the short arm of chromosome 6 . In 1996, HFE, a gene for HH, was found to have two missense mutations . A mutation at amino acid 282 (C282Y) was found to be homozygous in 83 percent of patients with HH. This is a point mutation from guanine to adenine, resulting in a missense mutation from cysteine to tyrosine. Such mutatio...
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[GWAS:Hemoglobin levels]
normal/common
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rs6025 represents a SNP in the Factor V F5 gene, encoding a change in the protein from an arginine at position 506 to a glutamine. The resulting rs6025(A) allele encodes a mutation known as the Leiden mutation, R506Q, found in perhaps 3 to 5% of the individuals in most populations. About 1 in 10 individuals harboring the R506Q will experience clinically significant venous thromboembolism in their lifetimes (according to OMIM). Overall, the rs6025(A) allele appears to be necessary but not sufficient for the development of venous thromboembolism. Patients who are rs6025(A;G) heterozygotes but lack other risk-enhancing SNPs have a risk of recurrent deep venous thrombosis equal to patients with no such SNPs. In contrast, patients who are heterozygotes for both rs6025 and the prothrombin rs1799...
5 snps
(hide) Gs240
slightly increased risk for autism
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A common SNP in the CNTNAP2 gene, rs7794745, is associated with increased risk for autism based on a study of 148 affected children from families with two more autistic children. Related article A genome-wide association study of autism reveals a common novel risk locus at 5p14.1. Do candidate genes discriminate patients with an autism spectrum disorder from those with attention deficit/hyperactivity disorder and is there an effect of lifetime substance use disorders? A common genetic variant in the neurexin superfamily member CNTNAP2 is associated with increased risk for selective mutism and social anxiety-related traits. Genetic variation in CNTNAP2 alters brain function during linguistic processing in healthy individuals. [PharmGKB:Curated This common variant in CNTNAP2 is significantl...
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nature The inheritance of the AC haplotype of rs1861972 – rs1861973 in en2, the C allele of rs1811399 in npas2, and the C allele of rs1234747 may contribute to autism by affecting microRNA rs1861972(A) + rs1861973(C) haplotype assoc. with '''protective''' effect against autism in a study of 818 Han Chinese (184 diag. autistics, 225 unrelated volunteers, 409 randomly selected) [OMIM:ENGRAILED 2; EN2]
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mentioned by gs240
Frequency: 22.1%
References:3
References:3
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Haplotype rs12740310*C-rs3737296*G-rs12410279*A was overtransmitted (p(corrected)=0.0016), with a relative risk for autism of 1.8 in homozygous carriers [OMIM:MAP/MICROTUBULE AFFINITY-REGULATING KINASE 1; MARK1]
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mentioned by gs240 Association of autism with polymorphisms in the paired-like homeodomain transcription factor 1 (PITX1) on chromosome 5q31: a candidate gene analysis. Assessing the impact of a combined analysis of four common low-risk genetic variants on autism risk.
5 snps
(hide) Gs247
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[GWAS:None]
normal risk of developing Parkinson's Disease
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People with two copies of the T allele at rs6812193 appear to have a slightly lower risk of Parkinson's disease. The same researchers identified another risk allele for Parkinson's disease at rs11868035. plos [GWAS:Parkinson's disease]
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Mentioned in the 23andMe Parkinson's disease patent along with rs10513789
3 snps
(hide) Hair
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[GWAS:Hair morphology]
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[GWAS:Hair morphology]
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[GWAS:Hair morphology]
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[GWAS:Hair morphology]
Frequency: 30.1%
References:1
References:1
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[GWAS:Hair morphology]
7 snps
(hide) Hair color
Generally European; Light skin; Possibly an increased risk of melanoma This SNP is associated with skin, hair, and eye colour, and risk of melanoma. Individuals with the G;G genotype are generally of European descent and have fair skin. In a population-based case-control study investigating a number of pigmentation-related SNPs and their correlation with cutaneous malignant melanoma (CMM) in a Caucasian Australian population, rs16891982 (variant F374L) was found to be associated with odds ratios of 3.44, 2.86, 1.68, and 1.68 for all study subjects (1,738 CMM cases and 4,517 controls); subjects with northern European ancestry (1,438 cases and 3,098 controls); northern European subjects adjusted for hair, eye, and skin colour; and northern European subjects adjusted for the MC1R genotype, r...
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This snp influences skin pigmentation. The allele p.L374F indicates light-skinned european ancestry c.1122C>G, p.Phe374Leu (NCBI dbSNP rs16891982) in SLC45A2 was associated with protection from malignant melanoma (OR, 0.41; 95% CI, 0.24-0.70; P=0.008 after adjustment for multiple testing) An association study conducted on a population of European origin concluded that the rare (in Europeans, at least) allele L374, i.e. rs16891982(C) in dbSNP orientation, significantly increases the possibility of having black hair color, with an odds ratio of around 7. This population-based case-control study investigated a number of pigmentation-related SNPs and their correlation with cutaneous malignant melanoma (CMM) in an Australian population. rs16891982 (variant F374L) was found to be associated w...
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[GWAS:Hair color]
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[GWAS:Hair color]
Frequency: 65.2%
References:1
References:1
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[GWAS:Hair color]
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rs1805005, known as Val60Leu or V60L, is a SNP in the MC1R gene associated with light blond hair color in one study. The risk allele is rs1805005(T), compared with the wild-type rs1805005(G) allele. See also OMIM 155555.0006 [OMIM:?]
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plos the association between rs12203592 and hair color was independent of rs1540771, a SNP between the IRF4 and EXOC2 genes previously found to be associated with hair color. [PharmGKB:Non-Curated GWAS Results: Genetic determinants of hair, eye and skin pigmentation in Europeans (Initial Sample Size: 2,986 individuals; Replication Sample Size: 3,932 individuals). This variant is associated with freckles.] [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 8; SHEP8] [GWAS:Freckles]
7 snps
(hide) Hair curliness
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rs499697 the minor, derived allele is associated with curlier hair curl, 0.13 points per G. [GWAS:Common traits (Other)]
1 snp
(hide) Haplogroup R (Y-DNA)
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common on affy axiom data
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Since R1b1c is very common, the first interesting discovery involved a SNP in that haplogroup, rs34276300, which was found to be ancestral in one branch of R1b1c and derived in several other branches. According to [https://www.23andme.com/you/community/thread/1144/ a 23andMe discussion, this is one of the SNPs that were re-analyzed in April 2009. Customers with older data may wish to redownload. SNPs affected: * rs4420638 * rs34276300 * rs3091244 * rs34601266 * rs2033003 * rs7900194 * rs9332239 * rs28371685 * rs1229984 * rs28399504. [haplogroup:?]
15 snps
(hide) Haplogroup Y (Y-DNA)
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
References:2
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[haplogroup:?]
References:0
References:1
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[haplogroup:?]
References:1
References:0
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[haplogroup:?]
References:1
References:0
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[haplogroup:?]
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[haplogroup:?]
References:3
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[haplogroup:?]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common on affy axiom data
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Since R1b1c is very common, the first interesting discovery involved a SNP in that haplogroup, rs34276300, which was found to be ancestral in one branch of R1b1c and derived in several other branches. According to [https://www.23andme.com/you/community/thread/1144/ a 23andMe discussion, this is one of the SNPs that were re-analyzed in April 2009. Customers with older data may wish to redownload. SNPs affected: * rs4420638 * rs34276300 * rs3091244 * rs34601266 * rs2033003 * rs7900194 * rs9332239 * rs28371685 * rs1229984 * rs28399504. [haplogroup:?]
45 snps
(hide) Haplogroups
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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haplogroups
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haplogroups
Frequency: 100.0%
References:0
References:0
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haplogroups
Frequency: 100.0%
References:0
References:0
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haplogroups
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common on affy axiom data
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Since R1b1c is very common, the first interesting discovery involved a SNP in that haplogroup, rs34276300, which was found to be ancestral in one branch of R1b1c and derived in several other branches. According to [https://www.23andme.com/you/community/thread/1144/ a 23andMe discussion, this is one of the SNPs that were re-analyzed in April 2009. Customers with older data may wish to redownload. SNPs affected: * rs4420638 * rs34276300 * rs3091244 * rs34601266 * rs2033003 * rs7900194 * rs9332239 * rs28371685 * rs1229984 * rs28399504. [haplogroup:?]
21 snps
(hide) HLA
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People with one or two copies of the G allele at this SNP are 3.5 times more likely to suffer liver injury than TT carriers when taking the prescription nonsteroidal anti-inflammatory drug (NSAID) lumiracoxib. This new pain medication was approved in Europe in late 2006, but because of a higher incidence of liver injury and patient deaths than among patients using other NSAIDs, it was withdrawn from the market in most countries. It is still sold in some countries under the brand names Prexige and Joicela.
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This SNP is associated with a higher risk of liver injury in patients taking the nonsteroidal anti-inflammatory drug lumiracoxib, which has been withdrawn from most markets.
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Mapping the genetic architecture of gene expression in human liver. Association of MHC SNP genotype with susceptibility to type 1 diabetes: a modified survival approach. A large-scale replication study identifies TNIP1, PRDM1, JAZF1, UHRF1BP1 and IL10 as risk loci for systemic lupus erythematosus. Quantitative trait loci for CD4:CD8 lymphocyte ratio are associated with risk of type 1 diabetes and HIV-1 immune control. Genome-wide association study in Asian populations identifies variants in ETS1 and WDFY4 associated with systemic lupus erythematosus. The effect of single nucleotide polymorphisms from genome wide association studies in multiple sclerosis on gene expression. An application of Random Forests to a genome-wide association dataset: methodological considerations & new findings. D...
3 snps
(hide) Intelligence
The (A;G) genotype averages 2.8 PIQ points higher than the (G;G), but averages 2.84 PIQ points lower than (A;A) genotype
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SNPs in the SNAP25 gene were initially linked to intelligence but have failed to replicate . While now suspect, the original work can be found in . The (A;A) genotype averaged 2.84 PIQ points higher than the (A;G) genotype, which averages 2.8 PIQ points higher than the (G;G) genotype (p=0.0002). Variance in this SNP may account for 3.4% of the phenotypic variance in PIQ. rs363050 is in close linkage with rs353016, with r2 = 0.98, such that the rs363050(A) allele typically is linked to the rs353016(T) allele. For SNPs rs363039 - rs363043 - rs353016, respectively, the haplotype C-T-T is most associated with higher intelligence in children, whereas the haplotype C-C-T is most associated in adults (SNPs oriented as in dbSNP). Measures of Intelligence
very slight descrease in cortical thickness and IQ; see full description
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rs7171755 is a SNP near the synaptic cell adhesion glycoprotein-encoding NPTN gene. A study of ~1,500 adolescents determined that the rs7171755(A) allele is associated with a slightly thinner left hemisphere cortex and also a slight decrease in verbal and nonverbal intelligence (IQ). The differences were really quite slight; each copy of the risk allele decreased cortical thickness by 0.7%, and decreased verbal and nonverbal IQ by 1.8 and 1.4 points, respectively. This study awaits independent replication. Also, note that eight SNPs in the NPTN locus were reported as jointly showing significant association with cortical thickness in addition to rs7171755: rs7176637, rs11854138, rs8028749, rs12185108, rs1564492, rs899981, rs7178269 and rs4075802.
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non sig. gwas, hit (p = 3 x 10^-6) - Digit Symbol [GWAS:Cognitive Performance]
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non sig. gwas, hit (p = 4 x 10^-7) for backwards digit span [GWAS:Cognitive Performance]
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non sig. gwas, hit (p = 4 x 10^-6) for PC1 (principal component 1) among the cognitive tests performed [GWAS:Cognitive Performance]
Frequency: 43.4%
References:1
References:1
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non sig. gwas, hit (p = 4 x 10^-6) for Trails A performance [GWAS:Cognitive Performance]
References:1
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non sig. gwas, hit (p = 5 x 10^-6) for spatial working memory (SWM) strategy in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
4+ IQ points for breastfeeding
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4+ IQ points for breastfeeding with the AA or AG genotypes Breastfeeding and IQ [GWAS:Response to statin therapy]
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rs174575, has been investigated with respect to increased intelligence in breastfed children but not yielded any clear result. *Although there was no difference in IQ linked to the SNP alone, breastfed children carrying one or two copies of rs174575(C) had a significant (6 point) increase in IQ compared to carriers of the same allele who were not breastfed. For children who were homozygous non-carriers, i.e. rs174575(G;G) individuals, there was no effect of breastfeeding on IQ. *did not replicate those findings. In contrast to their study, (G;G) children exhibited the greatest difference between feeding methods such that breastfed children performed similarly irrespective of child genotype whereas formula fed (G;G) children performed worse than other children on formula milk Breastfeeding ...
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non sig. gwas, top 25 GEE p-values, Boston Naming Test [GWAS:Cognitive test performance]
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non sig. gwas, top 25 GEE p-values, measure of attention and executive function [GWAS:Cognitive test performance]
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[GWAS:Cognitive performance]
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non sig. gwas, top 25 GEE p-values, Wide-Range Achievement Test [GWAS:Cognitive test performance]
Frequency: 41.6%
Repute:Good
References:0
Repute:Good
References:0
Slightly higher intracranial volume
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associated with intracranial volume (12q14.3; N = 15,782; P = 1.12 × 10−12) http://www.genomesunzipped.org/2012/04/another-iq-gene-new-methods-old-flaws.php (C;C) has higher cranial capacity (about 2 teaspoons) and over 2% higher IQ. (C;T) is half this positive effect. Intelligence
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non sig. gwas, hit (p = 1 x 10^-6) for pattern recognition memory (PRM) percent correct in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
Frequency: 38.9%
References:1
References:1
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non sig. gwas, hit (p = 5 x 10^-6) for intra-extra dimensional set shift (IED) EDS errors in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
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non sig. gwas, hit (p = 9 x 10^-6) principal component 1 (PC1) - CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
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[GWAS:Cognitive performance]
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[GWAS:Cognitive performance]
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non sig. gwas, hit (p = 1 x 10^-6) for forward digit span [GWAS:Cognitive Performance]
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non sig. gwas, hit (p = 2 x 10^-6) for forward digit span [GWAS:Cognitive Performance]
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non sig. gwas, top 25 GEE p-values, visual memory and organization [PharmGKB:Non-Curated GWAS results: Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study (Initial Sample Size: 705 individuals (Framingham); Replication Sample Size: NR). This variant is associated with Cognitive test performance.] [GWAS:Cognitive test performance]
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non sig. gwas, hit (p = 4 x 10^-6) for Test Trails A performance [GWAS:Cognitive Performance]
Frequency: 63.1%
References:1
References:1
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[GWAS:Cognitive performance]
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non sig. gwas, hit (p = 8 x 10^-6) for verbal recognition memory (VRM) free recall in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
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non sig. gwas, hit (p = 6 x 10^-6) for spatial span (SSP) length in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
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non sig. gwas, top hit for rapid visual information processing (RVP) hit probability in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
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This is one of four SNPs in the first intron of the SNAP25 gene that have been correlated with increased intelligence based on studies of ~300 Caucasian subjects. In orientation to the dbSNP entry for this SNP, rather than as published, the (C;C) genotype averages ~2 PIQ points higher than the (C;T) genotype, which averages 2 PIQ points higher than the (T;T) genotype. For SNPs rs363039 - rs363043 - rs353016, respectively, the haplotype C-T-T is most associated with higher intelligence in children, whereas the haplotype C-C-T is most associated in adults (SNPs oriented as in dbSNP).
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[GWAS:Cognitive performance]
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non sig. gwas, hit (p = 5 x 10^-6) for forward digit span [GWAS:Cognitive Performance]
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non sig. gwas, hit (p = 2 x 10^-6) for intra-extra dimensional set shift (IED) EDS errors in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
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non sig. gwas, hit (p = 4 x 10^-6) for intra-extra dimensional set shift (IED) EDS errors in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
Frequency: 13.3%
References:1
References:1
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non sig. gwas, hit (p = 6 x 10^-6) for paired associates learning (PAL) total errors at 8 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
Frequency: 23.9%
References:1
References:1
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non sig. gwas, hit (p = 3 x 10^-6) for intra-extra dimensional set shift (IED) EDS errors in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
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non sig. gwas, hit (p = 4 x 10^-6) for backwards digit span [GWAS:Cognitive Performance]
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non sig. gwas, hit (p = 8 x 10^-6) - Animals [GWAS:Cognitive Performance]
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non sig. gwas, hit (p = 1 x 10^-6) - Animals [GWAS:Cognitive Performance]
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non sig. gwas, hit (p = 5 x 10^-6) for Trails B performance [GWAS:Cognitive Performance]
Frequency: 38.9%
References:1
References:1
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[GWAS:Cognitive performance]
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non sig. gwas, hit (p = 2 x 10^-6) - Delayed Story Recall [GWAS:Cognitive Performance]
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[GWAS:Cognitive performance]
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non sig. gwas, top 25 GEE p-values, Boston Naming Test [GWAS:Cognitive test performance]
References:1
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non sig. gwas, hit (p = 4 x 10^-6) - Delayed Story Recall [GWAS:Cognitive Performance]
Frequency: 18.8%
References:1
References:1
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non sig. gwas, hit (p = 8 x 10^-6) for Controlled Oral Word Association (COWA) test performance [GWAS:Cognitive Performance]
Frequency: 30.8%
References:1
References:1
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non sig. gwas, top 25 GEE p-values, visual memory and organization [GWAS:Cognitive test performance]
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[GWAS:Educational attainment]
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Mentioned in retracted non sig. gwas, hit (p = 1 x 10^-6) for paired associates learning (PAL) total errors at 8 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
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non sig. gwas, hit (p = 3 x 10^-6) - Symbol Search [GWAS:Cognitive Performance]
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[GWAS:Cognitive performance]
Frequency: 23.2%
References:1
References:1
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non sig. gwas, hit (p = 5 x 10^-6) for paired associates learning (PAL) total errors at 8 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
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non sig. gwas, hit (p = 6 x 10^-6) - Animals [GWAS:Cognitive Performance]
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non sig. gwas, hit (p = 5 x 10^-6) for Trails B performance [GWAS:Cognitive Performance]
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non sig. gwas, hit (p = 3 x 10^-6) for Trails B performance [GWAS:Cognitive Performance]
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non sig. gwas, top hit for pattern recognition memory (PRM) percent correct in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
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non sig. gwas, hit (p = 3 x 10^-6) for Trails B performance [GWAS:Cognitive Performance]
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non sig. gwas, top hit for spatial working memory (SWM) 'between for 8 box stage' in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
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non sig. gwas, hit (p = 3 x 10^-6) - Animals [GWAS:Cognitive Performance]
Frequency: 46.9%
References:1
References:1
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[GWAS:Cognitive performance]
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intelligence related [PharmGKB:Curated Several studies showed an associaction of this SNP in DTNBP1 with schizophrenia and other psychotic disorders, including substance-induced psychosis]
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non sig. gwas, hit (p = 7 x 10^-6) for spatial working memory (SWM) strategy in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
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[GWAS:Cognitive performance]
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non sig. gwas, hit (p = 5 x 10^-6) for paired associates learning (PAL) total errors at 8 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
Frequency: 40.0%
References:1
References:1
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non sig. gwas, hit (p = 4 x 10^-6) for Trails A performance [GWAS:Cognitive Performance]
Frequency: 36.3%
References:1
References:1
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non sig. gwas, hit (p = 6 x 10^-6) for spatial working memory (SWM) strategy in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
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non sig. gwas, hit (p = 4 x 10^-6) for Stroop test performance [GWAS:Cognitive Performance]
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non sig. gwas, top 25 GEE p-values, visual memory and organization [GWAS:Cognitive test performance]
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non sig. gwas, top hit for spatial recognition memory (SRM) percent correct in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
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In 2009, a large, multi-sample replication study failed to find any significant association with Intelligence for this or other SNPs in CHRM2 . Earlier work had observed that this snp (and perhaps its neighbors) influenced intelligence and alcohol dependence CHRM2 gene predisposes to alcohol dependence, drug dependence and affective disorders: results from an extended case-control structured association study. And the earlier and or this pdf poster show association between the CHRM2 gene and intelligence . In this study of ~300 Caucasians, the (T;T) genotype appeared to typically have a 4 point higher IQ than the (A;T) genotype, which had a 4 point higher IQ (on average) than the (A;A) genotype. A nearby SNP, rs324640, showed similar results to rs324650, and was in linkage disequilibrium (...
common on affy axiom data
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non sig. gwas, hit (p = 5 x 10^-6) for PC1 (principal component 1) among the cognitive tests performed [GWAS:Cognitive Performance]
common in complete genomics
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non sig. gwas, hit (p = 3 x 10^-6) - Animals [GWAS:Cognitive Performance]
common in complete genomics
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non sig. gwas, top 25 GEE p-values, Boston Naming Test [PharmGKB:Non-Curated GWAS results: Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study (Initial Sample Size: 705 individuals (Framingham); Replication Sample Size: NR). This variant is associated with Cognitive test performance.] [GWAS:Cognitive test performance]
common in complete genomics
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non sig. gwas, hit (p = 4 x 10^-6) for intra-extra dimensional set shift (IED) EDS errors in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
common in complete genomics
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non sig. gwas, top 25 GEE p-values, visual memory and organization [GWAS:Cognitive test performance]
73 snps
(hide) Memory
normal confers susceptibility for the development of sporadic CJD
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rs1799990, also known as Met129Val or M129V, is a SNP in the prion protein PRNP gene. The more common rs1799990(A) allele encodes the Met (methionine). Historically, since 1991 this SNP has been associated with risk for sporadic Creutzfeldt-Jakob disease, with homozygotes of both types apparently at increased risk compared to heterozygotes. More recently, this SNP has been related to long-term memory with (A;A) and (A;G) individuals recalling 17% more words than (G;G) individuals at 24h following learning. A further study of 12 individuals of each of the 3 possible genotypes showed that at both 30 minutes and 24 hour time lags, correlations between retrieval-related brain activity and retrieval success were negative for (G;) homozygotes (the more activity, the worse retrieval success), whi...
References:2
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in all 4 ind. samples (1699 total indv.) associated with immediate recall, minor allele (C) carriers displayed worse short-term memory performance in a per allele fashion per HapMap data, the haplotype containing the C allele is in high LD with a (23andMe covered) haplotype consisting of rs4667867(A) (r^2 = 1), rs13421166(C), rs2126152(T), rs6432860(A) (+ the annotated SNP rs3812718(C) ) in the CEU+TSI sample
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anxiety-related personality traits, ADHD, schizophrenia part of a three marker haplotype rs737865-rs4680-rs165599 epistasis between SNPs in COMT (rs2097603, Val158Met (rs4680), rs165599) and polymorphisms in other schizophrenia susceptibility genes popular in pubmed is associated with bipolar disorder and influences prefrontal aspects of verbal memory in bipolar patients and healthy controls. [PharmGKB:Curated In a study of 78 African American and 65 white patients diagnosed with schizophrenia or schizoaffective disorder, this SNP in the COMT gene was found to have significant associations with response to risperidone over 2-12 weeks in both African-American and white patients.] [OMIM:CATECHOL-O-METHYLTRANSFERASE; COMT]
3 snps
(hide) Mendeliome
Generally European; Light skin; Possibly an increased risk of melanoma This SNP is associated with skin, hair, and eye colour, and risk of melanoma. Individuals with the G;G genotype are generally of European descent and have fair skin. In a population-based case-control study investigating a number of pigmentation-related SNPs and their correlation with cutaneous malignant melanoma (CMM) in a Caucasian Australian population, rs16891982 (variant F374L) was found to be associated with odds ratios of 3.44, 2.86, 1.68, and 1.68 for all study subjects (1,738 CMM cases and 4,517 controls); subjects with northern European ancestry (1,438 cases and 3,098 controls); northern European subjects adjusted for hair, eye, and skin colour; and northern European subjects adjusted for the MC1R genotype, r...
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This snp influences skin pigmentation. The allele p.L374F indicates light-skinned european ancestry c.1122C>G, p.Phe374Leu (NCBI dbSNP rs16891982) in SLC45A2 was associated with protection from malignant melanoma (OR, 0.41; 95% CI, 0.24-0.70; P=0.008 after adjustment for multiple testing) An association study conducted on a population of European origin concluded that the rare (in Europeans, at least) allele L374, i.e. rs16891982(C) in dbSNP orientation, significantly increases the possibility of having black hair color, with an odds ratio of around 7. This population-based case-control study investigated a number of pigmentation-related SNPs and their correlation with cutaneous malignant melanoma (CMM) in an Australian population. rs16891982 (variant F374L) was found to be associated w...
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[OMIM:?]
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Susceptibility genes for gentamicin-induced vestibular dysfunction.
normal
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This SNP lies within the gene coding for ATM (Ataxia telegensia mutated), a main role of which is the repair of double-stranded DNA breaks. As such SNPs within this gene have been associated with susceptibility to cancer. Rs1801516(A,A) leads to homozygous expression of ATM(D1853N). Homozygotes for this mutation have been associated with increased likelihood of pancreatic cancer (OR, 2.55; 95% CI, 1.08-6.00; P = 0.032) . Despite early reports, the role of Rs1801516 in breas cancer is unclear . A meta-analysis concluded that this mutation was not a risk factor for developing breast cancer (GA vs GG:OR=1.18 (95%CI 0.90-1.53); AA vs GG:OR=0.77 (95%CI 0.58-1.03) . Similarly the (A,A) variant has been reported to be protective against Melanoma development (p=3.4×10−9, OR=0.84 overall...
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[OMIM:MYOCARDIAL INFARCTION, DECREASED SUSCEPTIBILITY TO]
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Development of a fingerprinting panel using medically relevant polymorphisms. Genetic risk factors for hepatopulmonary syndrome in patients with advanced liver disease. Population based allele frequencies of disease associated polymorphisms in the Personalized Medicine Research Project. Genetic variants associated with Von Willebrand factor levels in healthy men and women identified using the HumanCVD BeadChip. von Willebrand factor plasma levels, genetic variations and coronary heart disease in an older population. [GWAS:Coagulation factor levels]
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15,000 individuals. Each copy of the minor T allele of SNP rs2228671 was related to a decrease of LDL-C levels by 0.19 mmol/L (95% confidence interval (CI) [0.13-0.24] mmol/L, p = 1.5x10(-10)) and a significantly lower risk of coronary artery disease (OR per copy of the T allele: 0.82, 95% CI [0.76-0.89], p = 2.1x10(-7)) [PharmGKB:Non-Curated GWAS results: Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. (Initial Sample Size: 17,797 individuals; Replication Sample Size: NR); (Region: 19p13.2; Reported Gene(s): LDLR; Risk Allele: rs2228671-G); (p-value= 0.00000000000004).This variant is associated with LDL cholesterol.] [OMIM:LOW DENSITY LIPOPROTEIN RECEPTOR; LDLR] [GWAS:Cholesterol, total]
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[OMIM:?]
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age related macular degeneration [OMIM:COMPLEMENT FACTOR H; CFH]
Frequency: 2.7%
References:0
References:0
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[OMIM:?]
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[OMIM:?]
normal risk for Alzheimer's; higher total and LDL cholesterol in females
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RNA made containing the rs688(T) SNP, a variant near exon 12 of the low-density lipoprotein receptor (LDLR) that is a receptor for ApoE proteins, is spliced at lower efficiency in males. Presumably due to this, the rs688(T;T) genotype was associated with increased risk for Alzheimer's disease odds in males (odds ratio 1.49, CI: 1.13-1.97, uncorrected p=0.005), but not in females. The presence of the rs688(T) allele associates with increased total and LDL-cholesterol in female members of the Framingham Offspring Study; rs688 was not associated with significant differences in HDL-cholesterol. The largest rs688-associated cholesterol differences were observed in pre-menopausal women. Taken together, rs688, a SNP present in approximately 60% of Caucasians, is associated with significant 10% in...
common/normal
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Note that this SNP is unusual in at least two regards. First, it is defined in both dbSNP and here in SNPedia (currently at least) as being on the minus strand, even though the vast majority of its fellow CYP21A2 gene SNPs are defined on the plus strand. The literature and most (other) databases define this SNP based on the plus strand. Second, there are three alleles for this SNP; as defined on the minus strand, there are plenty of individuals walking around with rs6467(G) and rs6467(T) alleles, both of which lead to fully functional 21-hydroxylase (the enzyme encoded by the CYP21A2 gene), and there are also some individuals carrying a rs6467(C) allele, which severely reduces enzyme activity. The rs6467(T) polymorphism defines the CYP21A2*1B allele according to the CYP21A2 Nomenclature ta...
18 snps
(hide) Menopause
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rs4806660 is a SNP on chromosome 19. A case control study of ~2,000 women found that each rs4806660(C) allele was associated with an average decrease in age at menopause of ~1 month. This also meant that each rs4806660(T) allele yielded an odds ratio of 1.45 (CI: 1.32–1.59, p = 8.88 x 10e-16) of not having early menopause, defined as occurring before the age of 46. Overall, women homozygous for the 'early' alleles at all 4 SNPs found in this study were ~4 times more likely to undergo menopause early compared to women who had a total of 3 or less risk alleles. However, the ability to predict which women will actually undergo early menopause using these 4 SNPs is still low. [OMIM:?]
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23andMe blog rs1172822(T) Menopause about 25 weeks earlier [OMIM:?] [GWAS:Menopause]
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[GWAS:Menopause]
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[OMIM:?] [GWAS:Menopause]
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[GWAS:Menopause]
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[GWAS:Menopause]
Frequency: 60.4%
References:1
References:1
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[GWAS:Menopause]
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[GWAS:Menopause]
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[GWAS:Menopause]
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23andMe blog rs365132(T) Menopause about 20 weeks later [OMIM:?] [GWAS:Menarche and menopause (age at onset)]
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rs244715 is a SNP on chromosome 5. A case control study of ~2,000 women found that each rs244715(T) allele was associated with an average increase in age at menopause of ~1 month. This also meant that each rs244715(C) allele yielded an odds ratio of 1.2 (CI: 1.09–1.32, p = 1.7 x 10e-4) of early menopause, defined as occurring before the age of 46. Overall, women homozygous for the 'early' alleles at all 4 SNPs found in this study were ~4 times more likely to undergo menopause early compared to women who had a total of 3 or less risk alleles. However, the ability to predict which women will actually undergo early menopause using these 4 SNPs is still low.
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rs9379896 is a SNP on chromosome 6. A case control study of ~2,000 women found that each rs9379896(C) allele was associated with an average increase in age at menopause of ~1 month. This also meant that each rs9379896(T) allele yielded an odds ratio of 1.13 (CI: 1.01–1.27, p = 3.8 x 10e-2) of early menopause, defined as occurring before the age of 46. Overall, women homozygous for the 'early' alleles at all 4 SNPs found in this study were ~4 times more likely to undergo menopause early compared to women who had a total of 3 or less risk alleles. However, the ability to predict which women will actually undergo early menopause using these 4 SNPs is still low.
14 snps
(hide) Mental health
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rs964201 and rs2442496 arose approximately 50,000 years ago and show strong positive selection in the lineage leading to humans [http://originsgenomeresources.net/musings/?p=68]
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origins associated with an independent aspect of decision making in a learning paradigm Association analysis of the protein phosphatase 1 regulatory subunit 1B (PPP1R1B) gene with nicotine dependence in European- and African-American smokers. Genetic analysis of the gene coding for DARPP-32 (PPP1R1B) in Japanese patients with schizophrenia or bipolar disorder. Reduced prefrontal cortex DARPP-32 mRNA in completed suicide victims with schizophrenia. The biological basis of anger: associations with the gene coding for DARPP-32 (PPP1R1B) and with amygdala volume. Dopaminergic genes predict individual differences in susceptibility to confirmation bias. Variation of the gene coding for DARPP-32 (PPP1R1B) and brain connectivity during associative emotional learning.
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origins blog linked to brain mophology via a haplotype block with rs833070 and rs2146323, Large-scale evaluation of candidate genes identifies associations between VEGF polymorphisms and bladder cancer risk. A genetic association analysis of cognitive ability and cognitive ageing using 325 markers for 109 genes associated with oxidative stress or cognition. Polymorphisms in the VEGFA and VEGFR-2 genes and neovascular age-related macular degeneration. Vascular endothelial growth factor gene polymorphisms and ovarian cancer survival. Genetics of VEGF serum variation in human isolated populations of cilento: importance of VEGF polymorphisms. Contribution of VEGF polymorphisms to variation in VEGF serum levels in a healthy population.
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g2b2mh blog rs833070 and rs2146323. Individuals with the CC genotype at rs833070 and rs2146323 displayed smaller hippocampal volumes than T-allele and A-allele carriers, respectively.
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associated with vulnerability to nicotine addiction in men. g2b2mh blog rs1044396 mediates effects of nicotine self-medication via parietal cortex. subjects with the (T;T) genotype showed robust brain activity in the parietal cortex while subjects with the (C;C) genotype showed very little change in activity. [PharmGKB:Curated This variant is closely linked to rs2236196 and has been associated with the intensification of nicotine dependence.] [OMIM:CHOLINERGIC RECEPTOR, NEURONAL NICOTINIC, ALPHA POLYPEPTIDE 4; CHRNA4]
common in complete genomics
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rs964201 is an A/G SNP located in the ASPM gene. The G-allele of this SNP as well as the A-allele of rs3762271 another SNP located in the ASPM gene and rs2442496 a SNP in the MCPH1 gene arose approximately 50,000 years ago and show strong positive selection in the lineage leading to humans. A comment is found at g2b2mh.
6 snps
(hide) Micronutrient Metabolism
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Association of a common nonsynonymous variant in GLUT9 with serum uric acid levels in old order amish.
4 snps
(hide) MicroRNA
~1.2x increased risk for cancer
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microRNA 1,009 breast cancer cases and 1,093 controls in a population of Chinese women *rs3746444 in hsa-mir-499 A>G OR 1.25; 95% CI, 1.02-1.51 Genetic variants of miRNA sequences and non-small cell lung cancer survival. MicroRNA polymorphisms: the future of pharmacogenomics, molecular epidemiology and individualized medicine. Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes. SNPs in human miRNA genes affect biogenesis and function. Common genetic variants in pre-microRNAs are associated with risk of coal workers' pneumoconiosis. MicroRNA polymorphisms: a giant leap towards personalized medicine. Common genetic variants in pre-microRNAs and risk of gallbladder cancer in North Indian population. Association of pre-microRNAs genetic varia...
0.58x decreased risk for esophageal cancer
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rs6505162 is a SNP located in the pre-miRNA region of mir423. The major allele is rs6505162(C). A study of 346 Caucasians with esophageal cancer found that compared with the homozygous wild-type genotype of rs6505162, individuals with the heterozygous and homozygous variant genotype had a significantly reduced esophageal cancer risk with odds ratios of 0.58 (CI: 0.41-0.82) and 0.43 (CI: 0.27-0.68), respectively. After stratifying by gender, smoking, and age, the authors discovered that the protective effect was significant only for individuals under 64 years of age, regardless of sex or whether they smoked. Other unfavorable genotypes (ie SNPs) were also identified that were not as significant as rs6505162, and the overall risk of esophageal cancer increased with increasing numbers of unfa...
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discussed in nature Single nucleotide polymorphisms of microRNA machinery genes modify the risk of renal cell carcinoma. Genetic variations in microRNA-related genes are novel susceptibility loci for esophageal cancer risk. Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes. Genetic Polymorphisms in MicroRNA-Related Genes as Predictors of Clinical Outcomes in Colorectal Adenocarcinoma Patients.
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schizophrenia, p = 1.6 x 10^-11, top hit in a rather large combined sample of (stage 1) 21,856 Europeans and (stage 2, replication) 29,839 independent individuals, see also this post on the Schizophrenia Research Forum Per the above reference, this SNP is located within an intron of miR-137 / MIR137 (on Wikipedia). Four other additional loci containing predictive targets of this microRNA also passed the threshold for genome-wide significance.. potentially suggesting some involvement of miR-137 mediated activity in the disease. Genome-wide supported variant MIR137 and severe negative symptoms predict membership of an impaired cognitive subtype of schizophrenia. [GWAS:Autism spectrum disorder, attention deficit-hyperactivity disorder, bipolar disorder, major depressive disorder, and schizop...
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nature The inheritance of the AC haplotype of rs1861972 – rs1861973 in en2, the C allele of rs1811399 in npas2, and the C allele of rs1234747 may contribute to autism by affecting microRNA rs1861972(A) + rs1861973(C) haplotype assoc. with '''protective''' effect against autism in a study of 818 Han Chinese (184 diag. autistics, 225 unrelated volunteers, 409 randomly selected) [OMIM:ENGRAILED 2; EN2]
2x higher ER- breast cancer risk
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microRNA 749 Swedish incident breast cancer cases with detailed clinical data and up to 15 years of follow-up together with 1493 matched controls. The strongest association was between the rs743554(T) allele of the ITGB4 gene and estrogen receptor negative (ER-) tumors (odds ratio 2.09, CI: 1.19-3.67) and worse survival compared to the wild type genotype carriers (hazard ratio [HR] 2.11, CI: 1.21-3.68). The poor survival was significantly associated with the aggressive tumour characteristics: high grade, lymph node metastasis and high stage.
Magnitude: 0
Frequency: 44.2%
References:62
Frequency: 44.2%
References:62
normal
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miRNA sequences and non-small cell lung cancer rs11614913 SNP in hsa-mir-196a2 was associated with survival in individuals with NSCLC. Specifically, survival was significantly decreased in individuals who were homozygous CC at SNP rs11614913. microRNA 1,009 breast cancer cases and 1,093 controls in a population of Chinese women *rs11614913 in hsa-mir-196a2 T>C 1.23; 95% confidence interval [CI], 1.02-1.48 *rs3746444 in hsa-mir-499 A>G OR 1.25; 95% CI, 1.02-1.51 Single nucleotide polymorphisms of microRNA machinery genes modify the risk of renal cell carcinoma. Genetic variations in microRNA-related genes are novel susceptibility loci for esophageal cancer risk. Signatures of purifying and local positive selection in human miRNAs. MicroRNA polymorphisms: the future of pharmacogenomics...
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nature The inheritance of the AC haplotype of rs1861972 – rs1861973, the C allele of rs1811399, and the C allele of rs1234747 may contribute to autism by affecting microRNA rs1861972(A) + rs1861973(C) haplotype assoc. with '''protective''' effect against autism in a study of 818 Han Chinese (184 diag. autistics, 225 unrelated volunteers, 409 randomly selected) [OMIM:ENGRAILED 2; EN2]
Magnitude: 0
Frequency: 90.0%
Repute:Good
References:1
Frequency: 90.0%
Repute:Good
References:1
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seems to have a microrna snp near 8q24 rs10109700 rs7832031
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seems to have a microrna snp near 8q24 rs10109700 rs7832031 Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers.
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nature The inheritance of the AC haplotype of rs1861972 – rs1861973, the C allele of rs1811399, and the C allele of rs1234747 may contribute to autism by affecting microRNA
normal
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(C;C) predisposes to papillary thyroid carcinoma. Among 42 patients with familial breast cancer and 82 patients with ovarian cancer, those with at least one rs2910164(C) SNP tended to have been diagnosed at an earlier age than those with only (G) alleles. For the breast cancer patients, the difference in median age was between 45 vs 56 (p = 0.029) and for ovarian cancer patients, 45 vs 50, (p = 0.014). (G;G) males were two-fold more susceptible to hepatocellular carcinoma (OR = 2.016, 95% CI = 1.056-3.848, P = 0.034) perhaps an ambiguous flip? [OMIM:MICRO RNA 146A; MIRN146A]
18 snps
(hide) Mitochondrial Haplogroup
Frequency: 9.4%
References:0
References:0
also known as is a mitochondrial snp 4917G PLoS this snp predicts the presence of age related macular degeneration (OR = 2.16, 95%CI 1.20–3.91, p = 0.01). This genotype is likely to have many other effects
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Also known as mitochondrial SNP 4917G. PLoS This SNP predicts the presence of age related macular degeneration (odds ratio = 2.16, CI: 1.20-3.91, p = 0.01). ThinkGene coverage
Frequency: 14.1%
References:1
References:1
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haplogroups
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haplogroups
References:0
Frequency: 100.0%
References:0
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haplogroups
Frequency: 100.0%
References:0
References:0
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haplogroups
10 snps
(hide) MtDNA Haplogroup
Frequency: 9.4%
References:0
References:0
also known as is a mitochondrial snp 4917G PLoS this snp predicts the presence of age related macular degeneration (OR = 2.16, 95%CI 1.20–3.91, p = 0.01). This genotype is likely to have many other effects
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Also known as mitochondrial SNP 4917G. PLoS This SNP predicts the presence of age related macular degeneration (odds ratio = 2.16, CI: 1.20-3.91, p = 0.01). ThinkGene coverage
Frequency: 14.1%
References:1
References:1
References:0
5 snps
(hide) Musical aptitude
Frequency: 54.5%
References:1
References:1
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Strong association for ability to discriminate pitch found in Finnish study of 767 individuals belonging in 76 families . Posterior probability of LD given as 34% to trait Carl Seashore's subtest of pitch SP, but 84% to overall tested musical aptitude. Situated in protocadherin 7 gene, PCDH7 which has been suggested to play a role in cochlear and amygdaloid complexes. A genome-wide linkage and association study of musical aptitude identifies loci containing genes related to inner ear development and neurocognitive functions
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Region with strongest linkage for ability to discriminate pitch found in study of 767 Finnish individuals belonging in 76 families , involved in musical aptitude. Posterior Probability of Linkage given as 86% to trait Carl Seashore's subtest of pitch (SP). Located next to the region harboring the protocadherin 7 gene, PCDH7 which has been suggested to play a role in cochlear and amygdaloid complexes. This SNP is in LIMCH1 LIM and calponin homology domains 1 gene, which is thought to be unlikely to be responsible, probably a combination of SNP's frequently inherited with it are involved. The study suggests rs13146789 in PCDH7 as one likely causal variant. A genome-wide linkage and association study of musical aptitude identifies loci containing genes related to inner ear development and neu...
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Strongest association with combined capacities for music perception (pitch, duration, sound patterns) found in study of 767 Finnish individuals belonging in 76 families , involved in musical aptitude. Posterior probability of LD 98%. This region is located a few dozen kilobases upstream of the GATA binding protein 2 GATA2 gene. GATA2 regulates the development of cochlear hair cells and the inferior colliculus (IC), which are important in tonotopic mapping. SNP is surrounded by known regulatory regions, and may itself be in one. A genome-wide linkage and association study of musical aptitude identifies loci containing genes related to inner ear development and neurocognitive functions
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Strongest association for ability to discriminate sound patterns found in study of 767 Finnish individuals belonging in 76 families , involved in musical aptitude. Posterior probability of LD 70% to trait Karma Music Test KMT. Long non-coding RNA not linked to any known gene, that may have expression in human brain. Near LRRIQ3 Leucine-rich repeats and IQ motif containing 3. A genome-wide linkage and association study of musical aptitude identifies loci containing genes related to inner ear development and neurocognitive functions
4 snps
(hide) NAT2
Increased risk of hearing loss 15.2x risk of Age Related Hearing Impairment(ARHI), also known as presbycusis. This applies to the European and Turkish, but not Finnish populations.
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rs1799930 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. Also known as G590A. The risk allele for this SNP is rs1799930(A). [PharmGKB:Curated in vitro study; PK: 22-fold reduction in Vmax vs wild type] [OMIM:?]
NAT2 Slow metabolizer
Most non-Scandinavian Caucasians and approximately half of African-Americans are slow metabolizers. This variation is important because of its primary role in the deactivation of many chemicals in the body's environment, including those produced by caffeine and cigarettes as well as aromatic amine and hydrazine drugs used medicinally. In general, slow metabolizers have higher rates of certain types of cancer and are more susceptible to side effects from chemicals metabolized by NAT2. This prediction and that of gs156 of NAT2 metabolizer phenotype is based on using 2 SNPs, rs1041983 and rs1801280. An alternative prediction of NAT2 metabolizer status based on using more SNPs (6) is used by genosets gs138, gs139, and gs140.
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rs1041983, also known as C282T, is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The allele associated with slow NAT2 metabolization for this SNP is rs1041983(T). Genosets gs154 and gs156 evaluate predicated NAT2 metabolizer phenotype based on rs1041983 and rs1801280. [PharmGKB:Curated in vitro study; PK: 22-fold reduction in Vmax vs wild type]
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rs1208 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1208(G). [PharmGKB:Curated in vitro study; PK: 20-fold reduction in Vmax vs wild type] [OMIM:?]
common in complete genomics Predicted to be a NAT2 slow metabolizer.
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With 99% sensitivity and 95% specificity, at least in Caucasian populations, rs1495741 is reported to classify the NAT2 phenotype of an individual; it therefore is a candidate to replace the 7-SNP panel used in genosets such as gs138, gs139, and gs140. The rs1495741(A;A), (A;G) and (G;G) genotypes predicted slow, intermediate, and rapid NAT2 acetylation phenotypes, respectively. [GWAS:None]
1 genoset 4 snps
(hide) NatGeo
Normal risk of sexual dysfunction when taking SSRI Antidepressants.
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rs6311 (-1438A>G / A-1438G or -1438G>A / G-1438A) is a SNP located upstream (and within the promoter region of) HTR2A. Multiple Regulatory Variants Modulate Expression of 5-Hydroxytryptamine 2A Receptors in Human Cortex. The minor A allele of rs6311 reduces expression of a previously unannotated extension of the 5' untranslated region of HTR2A mRNA. rs6311 together with rs6314 have a modest effect on depression severity, when examined in the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study. Three (rs643627-rs594242-rs6311: A-C-T), two (rs594242-rs6311: C-T) and a single functional (rs6311: T) marker were protective against suicidal behavior. The complementary markers (rs594242-rs6311: G-C and rs6311: C) were associated with increased risk for non-violent and impu...
1.2x higher risk for inflammatory bowel diseases
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rs689466 is a SNP in the COX-2 gene, also known as the prostaglandin-endoperoxide synthase 2 PTGS2 gene. A Scottish and Danish case-control study including 732 Crohn's disease (CD) cases, 973 ulcerative colitis (UC) cases, and 1157 healthy controls found that the rs689466(G) allele was associated with higher risk for ulcerative colitis and inflammatory bowel disease, especially among those who never smoked. The reported odds ratios were 1.25 and 1.47, rspectively. This allele was also associated with younger age at diagnosis and with extensive ulcerative colitis. Cyclooxygenase-2 polymorphisms in Parkinson's disease. Pyrosequencing of polymorphisms in the COX-2 gene (PTGS2) with reported clinical relevance. Association of polymorphisms in cyclooxygenase (COX)-2 with coronary and carotid ca...
Frequency: 51.3%
References:1
References:1
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[PharmGKB:Curated In a GWAS of 3497 Dutch subjects from the Netherlands Study of Depression and Anxiety or from the Netherlands Twin Registry, this SNP was found to be associated with Smoking Initiation (p = 0.00007691; OR for minor allele A:1.256)]
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[GWAS:None]
Frequency: 46.4%
References:6
References:6
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Association of Toll-like receptor 4 gene polymorphisms with normal tension glaucoma. Association analysis of Toll-like receptor 4 polymorphisms with autoimmune pancreatitis. Lack of association between toll-like receptor 4 gene polymorphisms and sarcoidosis-related uveitis in Japan. Traffic-related air pollution, oxidative stress genes, and asthma (ECHRS). Sequence variants in the TLR4 and TLR6-1-10 genes and prostate cancer risk. Results based on pooled analysis from three independent studies.
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[GWAS:None]
Frequency: 42.5%
References:1
References:1
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[GWAS:None]
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[GWAS:None]
References:1
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[GWAS:None]
Frequency: 62.8%
References:1
References:1
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[GWAS:None]
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associated with specific patterns of brain activity. rs3087454 rs1355920 rs7520974 rs885834
~10% more likely to respond to citalopram
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rs1954787, located in an intron of the GRIK4 gene, was found to be associated with a somewhat increased rate of successful response to treatment of depression with the drug citalopram. From the abstract of this article: 'The effect size of (this) GRIK4 marker alone was modest, but homozygote carriers of the treatment-response-associated marker alleles of both the GRIK4 and HTR2A (see rs7997012) genes were 23% less likely to experience nonresponse to (citalopram) treatment relative to participants who did not carry any of these marker alleles.' * See also Anxiety Blog posting [PharmGKB:Curated A study in 1,816 eligible patients from the STAR*D cohort found that genetic variation in a kainic acid-type glutamate receptor is reproducibly associated with response to the antidepressant citalopr...
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discussed in nature Single nucleotide polymorphisms of microRNA machinery genes modify the risk of renal cell carcinoma. Genetic variations in microRNA-related genes are novel susceptibility loci for esophageal cancer risk. Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes. Genetic Polymorphisms in MicroRNA-Related Genes as Predictors of Clinical Outcomes in Colorectal Adenocarcinoma Patients.
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[PharmGKB:Curated Risk or phenotype-associated allele: A allele. Phenotype: Decreased fasting insulin. Study size: 4681. Study population/ethnicity: Replication study of Swedish control subjects. Significance metric(s): p = 0.001. Type of association: FA; GN.]
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[GWAS:None]
Frequency: 36.3%
References:1
References:1
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[PharmGKB:Curated In a GWAS of 3497 Dutch subjects from the Netherlands Study of Depression and Anxiety or from the Netherlands Twin Registry, this SNP was found to be associated with Smoking Initiation (p = 0.000004333; OR for minor allele T:0.786)]
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[GWAS:None]
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[GWAS:None]
Frequency: 75.9%
References:1
References:1
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[GWAS:None]
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Association study of polymorphisms in the excitatory amino acid transporter 2 gene (SLC1A2) with schizophrenia.
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
References:1
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[PharmGKB:Curated In a GWAS of 3497 Dutch subjects from the Netherlands Study of Depression and Anxiety or from the Netherlands Twin Registry, this SNP was found to be associated with Smoking Initiation (p = 0.00004278; OR for minor allele C:1.255)]
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[PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: This SNP was associated with a greater reduction in total cholesterol after at least 1 week of statin use. This was not replicated in a second cohort. Study size: 546 (original cohort); 100 (replication cohort). Study population/ethnicity: People taking statins; age 55 or older; Rotterdam Study; Netherlands. Significance metric(s): p = 0.05 (original); p = 0.975 (replication) Type of association: PD.]
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Association study of mast cell chymase polymorphisms with atopy. Genetic-epidemiological evidence on genes associated with HDL cholesterol levels: a systematic in-depth review. Power of multifactor dimensionality reduction and penalized logistic regression for detecting gene-gene interaction in a case-control study. Impact of polymorphisms of the genes encoding angiotensin II-forming enzymes on the progression of IgA nephropathy.
Frequency: 35.4%
References:1
References:1
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[GWAS:None]
Frequency: 57.5%
References:1
References:1
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[PharmGKB:Curated Risk or phenotype-associated allele: not stated Phenotype: Using a Quantitative Transmission Disequilibrium Test (QTDT), this variant was significantly associated with etoposide toxicity based upon IC50 values in cell lines from 30 parent-child trios. In combination, rs10018204, rs11222869, rs16965867, rs1846644, and rs6539870 were significant predictors of etoposide IC50, accounting for 55% of the etoposide IC50 variation in Caucasians. Study size: 87. Study population/ethnicity: 87 European descent Caucasians. Significance metric(s): p = 0.00009. Type of association: FA; GN.]
References:1
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[GWAS:None]
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[GWAS:None]
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Meta-analysis of three genome-wide association studies identifies susceptibility loci for colorectal cancer at 1q41, 3q26.2, 12q13.13 and 20q13.33.
Frequency: 44.2%
References:1
References:1
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Gene-environment interaction effects on the development of immune responses in the 1st year of life. Algorithm for automatic genotype calling of single nucleotide polymorphisms using the full course of TaqMan real-time data. A functional SNP of interferon-gamma gene is important for interferon-alpha-induced and spontaneous recovery from hepatitis C virus infection. Interferon gamma allelic variants: sex-biased multiple sclerosis susceptibility and gene expression. Host genetic factors and vaccine-induced immunity to hepatitis B virus infection. A single nucleotide polymorphism (A --> G) in intron 3 of IFNgamma gene is associated with asthma. Host genetic factors and vaccine-induced immunity to HBV infection: haplotype analysis. IFNG genotype and sex interact to influence the risk of chi...
Frequency: 28.3%
References:1
References:1
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[GWAS:None]
Frequency: 40.2%
References:1
References:1
Frequency: 28.3%
References:1
References:1
Frequency: 1.8%
References:1
References:1
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[GWAS:None]
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[GWAS:None]
Frequency: 46.9%
References:0
References:0
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
Frequency: 23.4%
References:1
References:1
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[PharmGKB:Curated Risk or phenotype-associated allele: not stated Phenotype: Using a Quantitative Transmission Disequilibrium Test (QTDT), this variant was significantly associated with etoposide toxicity based upon IC50 values in cell lines from 30 parent-child trios. Study size: 87. Study population/ethnicity: 87 European descent Caucasians. Significance metric(s): p = 0.00006. Type of association: FA; GN.]
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[GWAS:None]
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Gene-nutrient interactions among determinants of folate and one-carbon metabolism on the risk of non-Hodgkin lymphoma: NCI-SEER case-control study.
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[GWAS:None]
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[PharmGKB:Curated This variant is significantly associated with late-onset Alzheimer disease (LOAD) in a GWAS study with 492 LOAD cases and 498 cognitive controls using Illumina's HumanHap550 beadchip.]
References:3
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:Colorectal cancer]
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Population substructure and control selection in genome-wide association studies.
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[PharmGKB:Curated Risk or phenotype-associated allele: not stated Phenotype: Using a Quantitative Transmission Disequilibrium Test (QTDT), this variant was significantly associated with etoposide toxicity based upon IC50 values in cell lines from 30 parent-child trios. Study size: 176. Study population/ethnicity: 87 European descent Caucasians and 89 Yorubans. Significance metric(s): p = 0.00007. Type of association: FA; GN.]
Frequency: 48.7%
References:1
References:1
References:0
Frequency: 20.4%
References:1
References:1
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
Frequency: 38.1%
References:1
References:1
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[GWAS:None]
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[GWAS:None]
References:0
Frequency: 20.4%
References:1
References:1
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[GWAS:None]
Frequency: 56.6%
References:0
References:0
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Follow-up examination of linkage and association to chromosome 1q43 in multiple sclerosis.
References:1
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[GWAS:None]
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[GWAS:None]
References:0
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Variants of CTGF are associated with hepatic fibrosis in Chinese, Sudanese, and Brazilians infected with schistosomes.
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[GWAS:None]
References:5
References:1
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[GWAS:None]
Frequency: 52.2%
References:1
References:1
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mentioned as potentially affecting grey matter volume, sample size tiny
References:1
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[GWAS:None]
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[GWAS:None]
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[GWAS:Periodontal disease-related phenotypes]
References:1
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
Frequency: 60.2%
References:2
References:2
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[GWAS:None]
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[GWAS:None]
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[GWAS:Cognitive performance]
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[PharmGKB:Curated This variant is significantly associated with late-onset Alzheimer disease (LOAD) in a GWAS study with 492 LOAD cases and 498 cognitive controls using Illumina's HumanHap550 beadchip.]
References:2
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Frequency: 14.2%
References:4
References:4
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[GWAS:Adiponectin levels]
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[GWAS:None]
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0.75x decreased risk for Non-hodgkin's lymphoma
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rs4833103 is a SNP located in a cluster of toll-like receptor genes. In a pooled analysis including three population-based case-control studies of Non-Hodgkin's lymphoma (1,946 cases, 1,808 controls), two SNPs in moderate linkage disequilibrium were significantly associated with NHL: rs10008492 (odds ratio for (C;T) genotype 1.12, CI: 0.97-1.30; OR(T;T) 1.40, CI: 1.15-1.71; p(trend)=0.001) and rs4833103 (OR(A;C) 0.75, CI: 0.64-0.88; OR(A;A) 0.74, CI: 0.62-0.90; p(trend)=0.002; p(dominant)=0.0002).
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[GWAS:None]
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Tooth Development [GWAS:None]
Frequency: 41.6%
References:0
References:0
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23andMe blog blood pressure
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[GWAS:None]
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mentioned by gs240
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[GWAS:None]
Frequency: 49.6%
References:1
References:1
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[GWAS:None]
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association with restless leg syndrome
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[GWAS:None]
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This SNP was identified as a 'core' SNP helping to define one (of nine total) runs of homozygosity (ROH) potentially associated with increased risk for schizophrenia. Each region consists of at least 100 consecutive SNPs, generally spanning 500KB or more, for which both chromosomes in an individual were homozygous. The overall odds ratio for schizophrenia associated with inheriting 1, 2, or 3 of these 9 ROHs was calculated to be 3.3, 5.4, or 24, respectively, with 95% confidence intervals of (1.9-5.7), (3.7-16.1), and (6.9-83.9), respectively. This particular SNP, rs7582658, was deemed to be the core SNP of a region on chromosome 2 with 274 SNPs spanning 2282KB from 2:188489676 to 2:190772106 (build 35). Potentially independent of the ROH, the risk allele for this SNP in the orientation as...
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[PharmGKB:Curated This variant is associated with hip fracture in a GWAS study consisting of 403 chinese females (266 with hip fracture and 177 control subjects).]
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rs231725 associated with primary biliary cirrhosis
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[GWAS:None]
Frequency: 44.2%
References:2
References:2
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[GWAS:None]
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[GWAS:None]
Frequency: 37.2%
References:2
References:2
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[GWAS:None]
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Lack of replication of genetic predictors for the rheumatoid arthritis response to anti-TNF treatments: a prospective case-only study. [PharmGKB:Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.00003; OR: 5.5 (1.8, 20.2)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.]
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[PharmGKB:Curated This variant is significantly associated with late-onset Alzheimer disease (LOAD) in a GWAS study with 492 LOAD cases and 498 cognitive controls using Illumina's HumanHap550 beadchip.]
Frequency: 42.5%
References:1
References:1
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[PharmGKB:Curated This variant is significantly associated with late-onset Alzheimer disease (LOAD) in a GWAS study with 492 LOAD cases and 498 cognitive controls using Illumina's HumanHap550 beadchip.]
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[GWAS:None]
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rs1741981 and rs2547547 influence risk for postoperative hepatocellular carcinoma tumor recurrence up to 2.2x Detection of fetomaternal genotype associations in early-onset disorders: evaluation of different methods and their application to childhood leukemia.
Frequency: 3.5%
References:1
References:1
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[GWAS:None]
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Comprehensive follow-up of the first genome-wide association study of multiple sclerosis identifies KIF21B and TMEM39A as susceptibility loci. [GWAS:None]
Frequency: 27.4%
References:1
References:1
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finds no association between rs11832 and pulmonary emphysema
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[PharmGKB:Curated In a GWAS of 3497 Dutch subjects from the Netherlands Study of Depression and Anxiety or from the Netherlands Twin Registry, this SNP was found to be associated with Smoking Initiation (p = 0.00007324; OR for minor allele A:0.804)]
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Multiplexed genotyping of ABC transporter polymorphisms with the Bioplex suspension array. Genetic variation and antioxidant response gene expression in the bronchial airway epithelium of smokers at risk for lung cancer.
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[GWAS:None]
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ADHD GIT1 is associated with ADHD in humans and ADHD-like behaviors in mice
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[GWAS:None]
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Elevated expression and genetic association links the SOCS3 gene to atopic dermatitis. Elevated expression and polymorphisms of SOCS3 influence patient response to antiviral therapy in chronic hepatitis C. Lack of association between the tagging SNP A+930-->G of SOCS3 and type 2 diabetes mellitus: meta-analysis of four independent study populations. Gene expression and hepatitis C virus infection. Polymorphisms near SOCS3 are associated with obesity and glucose homeostasis traits in Hispanic Americans from the Insulin Resistance Atherosclerosis Family Study.
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[GWAS:None]
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References:1
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[GWAS:None]
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[GWAS:Height]
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[PharmGKB:Curated Risk or phenotype-associated allele: A allele. Phenotype: The A allele rs2894342, which lies in the promoter of MLN, is associated with carbamazepine (CBZ)-induced maculopapular exanthema (MPE)/ hypersensitivity syndrome (HSS). Study size: 175. Study population/ethnicity: 31 CBZ-induced MPE/HSS cases and 144 CBZ-tolerant controls of Chinese descent. Significance metric(s): p = 0.00342, OR = 2.88. Type of association: GN; PD; TOX; ADR.]
Frequency: 10.6%
References:1
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References:1
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[GWAS:None]
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References:0
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[GWAS:Breast cancer]
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[GWAS:None]
References:1
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[PharmGKB:Curated This variant is associated with end-of-induction minimal risidual disease (MRD) in childhood acute lymphoblastic leukemia (ALL) from 2 independent cohorts (GWAS result). Risk Allele: T, MAF= 0.40, combined P value= 5.62E-04.]
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[GWAS:None]
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Identification of a novel risk locus for progressive supranuclear palsy by a pooled genomewide scan of 500,288 single-nucleotide polymorphisms. [GWAS:None]
Frequency: 48.7%
References:1
References:1
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[GWAS:None]
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Associated with bipolar disorder in individuals of European ancestry. [GWAS:Bipolar disorder and schizophrenia]
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[GWAS:None]
Magnitude: 0
Frequency: 46.9%
Repute:Good
References:1
Frequency: 46.9%
Repute:Good
References:1
Magnitude: 0
Frequency: 85.0%
Repute:Good
References:3
Frequency: 85.0%
Repute:Good
References:3
normal
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rs10754339 is a SNP in the V-set domain containing T cell activation inhibitor 1 VTCN1 gene, which is also known as B7-H4. A study of 500 Chinese Han women with breast cancer (and an equal number of matched controls) concluded that the rs10754339(A;G) genotype and G allele showed a significantly increased risk of breast cancer (odds ratio 1.455, CI: 1.119-1.892, and 1.325, CI: 1.073-1.637, respectively). Additionally, the rs10754339(G;G) genotype was significantly associated with lymph node metastasis and PR status, and the G allele and the (A;G) genotype were respectively associated with lymph node metastasis and ER status.
common in complete genomics
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Cytokine SNPs: Comparison of allele frequencies by race and implications for future studies.
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G-C-T-C haplotype of rs2340690-rs788016-rs2305560-rs2565163 has odds ratio of 1.91 (CI: 1.26-2.89, p=0.002) for coronary heart disease compared to G-T-T-C, based on a study of 1,000 Han Chinese patients and matched controls. * Note: Haplotype allele assignments may not be in dbSNP orientation.
Magnitude: 0
Frequency: 96.5%
Repute:Good
References:1
Frequency: 96.5%
Repute:Good
References:1
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[GWAS:None]
normal/common in clinvar Found in 56% of all Caucasians on average, this genotype leads to a relative risk of 1.00, which is the most common risk, for late-onset (adult) asthma.
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rs1837253 is a SNP found a bit upstream of the thymic stromal lymphopoietin TSLP gene on chromosome 5. The TSLP protein plays a role in inflammation of cells in the trachea and alveoli therefore may have a causative role in certain types of asthma. The rs1837253(T) allele has been found to reduce the risk of developing late-onset (adult) asthma in several studies, and it is recognized by the CPMC Study as one they report to their participants. [GWAS:None]
289 snps
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more able to detect β-ionone (floral) fragrance
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rs6591536, also known as N183D or Asn183Asp, is a SNP in the olfactory receptor, family 5, subfamily A, member 1 OR5A1 gene. The rs6591536(A) allele encodes the asparagine (N). Individuals vary in their ability to smell various odors, largely due to variations in their olfactory receptors. Carriers of one or two rs6591536(G) alleles can detect a particular compound, β-ionone, at levels two orders of magnitude lower than rs6591536(A;A) individuals. In fact, this study reports that 96% of the observed phenotypic variation is determined by this single SNP, making it nearly a completely Mendelian trait. People with high or low β-ionone sensitivity are found in all populations, and based on this SNP, variability was seen even in Neanderthal populations. Since rs6591536 determines ^...
Magnitude: 1
References:0
References:0
Frequency: 48.7%
References:1
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Frequency: 4.4%
References:0
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Frequency: 31.9%
References:0
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References:0
13 snps
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homozygous for C677T of MTHFR = 10-20% efficiency in processing folic acid = high homocysteine, low B12 and folate levels This is the homozygous form of the C677T allele for the MTHFR gene. It is found in approximately * 15% of Hispanic Americans * 12% of Caucasian Americans * 12% of Japanese * 6% of Germans * 3% of Asians * 2% of African Americans * 1% of Sub-Saharan Africans Numerous health effects are associated with this variant. * Hyperhomocysteinemia and neurologic disorders: a review. (2014). A review. Certain genetic factors also cause elevated homocysteine levels, such as C667T substitution of the gene encoding methylenetetrahydrofolate reductase. Elevated homocysteine has been observed in several medical conditions, such as cardiovascular disorders, atherosclerosis, myocardial i...
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer ** renal cancer * cleft lip and cleft palate * coronary artery disease * dementia * depression * hyperhomocysteinemia * migraine * neural tube d...
Mix of muscle types. Likely sprinter. Normal for white people. One working and one defective copy of the gene for alpha-actinin-3 in fast-twitch muscle fibres. This genotype may indicate somewhat impaired muscles, however many sprinters and some endurance athletes have this.
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This SNP, in the ACTN3 gene, encodes a premature stop codon in a muscle protein called alpha-actinin-3. The polymorphism alters position 577 of the alpha-actinin-3 protein. In the (C;C) genotype is often called RR. The truncated (T;T) is often called XX. (T;T) is under-represented in elite strength athletes, consistent with previous reports indicating that alpha-actinin-3 deficiency appears to impair muscle performance. The most common nucleotide at this position, (C), encodes an arginine (amino acid code R), the alternative T allele encodes a stop codon (X). Hence, the SNP is referred to as R577X, with homozygotes being either RR or XX and heterozygotes being RX. XX individuals completely lack the expression of alpha-actinin-3. An earlier report studying a relatively small number of Austr...
Carrier of one CYP1A2*1F allele; Slow Caffeine Metabolizer. One copy of the slow caffeine metaboliser SNP, and one copy of the fast version. This makes you more strongly affected by drinking coffee, as caffeine is broken down slower in the liver. Supposedly this increases the risk of heart attacks, although other studies show caffeine is generally good for the heart. It also makes caffeine more effective at preventing Breast Cancer, Alzheimer's Disease, and Parkinson's disease. Too much caffeine will shrink your breasts.
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rs762551, also known as -164A>C or -163C>A, is a SNP encoding the CYP1A2*1F allele of the CYP1A2 gene. For historic reasons, the rs762551(C) allele is considered the wild-type, even though it is the rarer allele in most populations. The rs762551(A) allele is the 'fast metabolizer' allele known as CYP1A2*1F; the (C) allele is by comparison a slower metabolizer of certain substrates (including caffeine). In terms of genotypes, only rs762551(A;A) individuals are considered fast metabolizers. Individuals who are rs762551(A;C) heterozygotes or rs762551(C;C) homozygotes are both considered slow metabolizers. The CYP1A2 gene encodes a member of the cytochrome p450 family of proteins, which metabolize nutrients and drugs. One well known substrate of CYP1A2 is caffeine; individuals who are ca...
1.45 ng/mL lower Vitamin B6 blood concentration
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This is one of the SNPs reported by NutraHacker. Genetics and genomics of human aging. [PharmGKB:Non-Curated The C allele of this SNP is associated with lower blood concentration of vitamin B6 (Combined studies of Tuscan Italians ( inCHIANTI:N =1175 and Progetto Nutrizione study:N = 687) found 1.45 ng/mL lower vitamin B6 per copy of C (p = 8.3 x 10 (-18)))] [OMIM:?] [GWAS:Folate pathway vitamins]
Reduced conversion of beta-carotene to retinol Reduced BCMO1 activity results in 32% lower ability to convert Beta-carotene to retinyl esters and higher serum beta-carotene levels. See also rs12934922.
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rs12934922 (R267S) and rs7501331 (A379V) double mutant have a reduced catalytic activity of beta-carotene by 57%. Female volunteers carrying the T variant of rs7501331 (379V) had a 32% lower ability to convert Beta-carotene, and those carrying at least one T in both SNPs show a 69% lower ability to convert Beta-carotene into retinyl esters. rs7501331: the frequency of the wild-type C allele and variant T allele was 76 and 24%, respectively; 56% of the population was CC wild-type genotype, and 39% was heterozygote CT with the TT variant present in 5% of the population. rs12934922: the frequency of the wild-type A allele and variant T allele was 58 and 42%, respectively; 38% of the population was AA wild-type genotype, 40% was heterozygote AT, and 22% was TT homozygote
higher risk for endometrial cancer
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rs4633 is a variant at codon 62 of the COMT gene, however, it does not change the amino acid sequence of the COMT protein. In a study of 150 (Caucasian) cases of endometrial cancer, a significant increase in rs4633(T;T) genotype was observed in patients compared to controls (OR = 2.39, CI: 1.31-4.37, p = 0.004). Furthemore, the frequency of the C-G haplotype of rs4633-rs4680 was significantly higher in controls (p < 0.0001) than in patients. This correlated with lower expression levels of the COMT protein in carriers of these alleles. pubmed 1180576 Schizophrenia Susceptibility Genetic basis for individual variations in pain perception and the development of a chronic pain condition [PharmGKB:Curated On the basis of subjects' pain responsiveness, haplotypes involving rs6269 (A/G), rs46...
Increased risk for anxiety disorders
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A study of patients with panic disorder or social anxiety disorder, both moderately heritable anxiety disorders, concluded that the rs140701(A) allele was associated with increased risk for both disorders. This SNP was actually part of a tightly linked haplotype A-A-G (for SNPs rs3794808, rs140701 and rs4583306, respectively) that had 1.7x increased risk for panic disorder (CI: 1.2-2.3).
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association with essential hypertension . Functional analysis showed that the C allele of rs2070762 functioned as an enhancer in the absence of binding by unidentified transcriptional repressor(s)
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This is one of the SNPs reported by NutraHacker.
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This is one of the SNPs reported by NutraHacker.
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rs731236 protection from breast cancer (OR=0.80, 95%CI=0.64-0.99; p= 0.047) [PharmGKB:Curated This variant was significantly associated with acquired resistance to clodronate treatment in Caucasian patients with Paget's disease of the bone]
Intermediate risk of low bone mineral density disorders
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rs1544410, also known as the BsmI polymorphism, is a SNP in the Vitamin D receptor (VDR). Multiple studies examining bone mineral density (BMD) in women have associated the A allele with increased risk of low BMD , , & . Additionally, A meta-analysis of 26 studies estimated a decreased risk of osteoporosis associated with the G;G genotype with an odds ratio of 0.61, 95% CI, 0.40-0.92 . rs1544410 increases susceptibility to Shorter stature for carriers of the A allele [PharmGKB:Curated This variant is associated with etidronate response in Caucasian (Slovenian) postmenopausal women (24 patients), with bb genotype associated with lower increase in bone mineral density (BMD) after bisphosphonate treatments.]
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This is one of the SNPs reported by NutraHacker.
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Yasko Methylation Catalyzes the hydrolysis of AdoHcy to adenosine and homocysteine. AdoHcy hydrolysis serves not only to sustain the flux of methionine sulfur toward cysteine, but is believed also to play a critical role in the regulation of biologic methylations.
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Yasko Methylation Catalyzes the hydrolysis of AdoHcy to adenosine and homocysteine. AdoHcy hydrolysis serves not only to sustain the flux of methionine sulfur toward cysteine, but is believed also to play a critical role in the regulation of biologic methylations. This is one of the SNPs reported by NutraHacker.
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Yasko Methylation Catalyzes the hydrolysis of AdoHcy to adenosine and homocysteine. AdoHcy hydrolysis serves not only to sustain the flux of methionine sulfur toward cysteine, but is believed also to play a critical role in the regulation of biologic methylations. This is one of the SNPs reported by NutraHacker.
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identifies a region associated with nicotine dependence in this particular study (1,050 dependents, 879 non-dependent controls, all of European descent), noted as distinct from the loci which rs16969968 defines Cholinergic nicotinic receptor genes implicated in a nicotine dependence association study targeting 348 candidate genes with 3713 SNPs. Variants in nicotinic receptors and risk for nicotine dependence. Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence. Genetic variability in nicotinic acetylcholine receptors and nicotine addiction: converging evidence from human and animal research. Familial aggregation of common sequence variants on 15q24-25.1 in lung cancer. Association of a single nucleotide polymorphism in neuronal...
Frequency: 10.6%
References:3
References:3
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Common variation in the beta-carotene 15,15'-monooxygenase 1 gene affects circulating levels of carotenoids: a genome-wide association study. Single nucleotide polymorphisms upstream from the beta-carotene 15,15'-monoxygenase gene influence provitamin A conversion efficiency in female volunteers. [OMIM:HYPERCAROTENEMIA AND VITAMIN A DEFICIENCY, AUTOSOMAL DOMINANT]
Reduced conversion of beta-carotene to retinol Associated with Rs7501331 and reduced BCMO1, lower ability to convert beta-carotene to retinyl esters and higher serum beta-carotene levels. See also Rs7501331
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rs12934922 (R267S) and rs7501331 (A379V) double mutant have a reduced catalytic activity of beta-carotene by 57%. Female volunteers carrying the T variant of rs7501331 (379V) had a 32% lower ability to convert Beta-carotene, and those carrying at least one T in both SNPs show a 69% lower ability to convert Beta-carotene into retinyl esters. rs7501331: the frequency of the wild-type C allele and variant T allele was 76 and 24%, respectively; 56% of the population was CC wild-type genotype, and 39% was heterozygote CT with the TT variant present in 5% of the population. rs12934922: the frequency of the wild-type A allele and variant T allele was 58 and 42%, respectively; 38% of the population was AA wild-type genotype, 40% was heterozygote AT, and 22% was TT homozygote
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ADHD GIT1 is associated with ADHD in humans and ADHD-like behaviors in mice
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Influence of child abuse on adult depression: moderation by the corticotropin-releasing hormone receptor gene. Association of FKBP5 polymorphisms and childhood abuse with risk of posttraumatic stress disorder symptoms in adults. Psychobiology and molecular genetics of resilience. Risk and resilience: genetic and environmental influences on development of the stress response. A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data. Effect of Childhood Trauma on Adult Depression and Neuroendocrine Function: Sex-Specific Moderation by CRH Receptor 1 Gene. Moderation of the association between childhood maltreatment and neuroticism by the corticotropin-releasing hormone receptor 1 gene. Association of CRHR1 and CRHR2 with major depressive disorder a...
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Influence of child abuse on adult depression: moderation by the corticotropin-releasing hormone receptor gene. Association of FKBP5 polymorphisms and childhood abuse with risk of posttraumatic stress disorder symptoms in adults. Risk and resilience: genetic and environmental influences on development of the stress response. A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data. The distribution and most recent common ancestor of the 17q21 inversion in humans. Effect of Childhood Trauma on Adult Depression and Neuroendocrine Function: Sex-Specific Moderation by CRH Receptor 1 Gene. Moderation of the association between childhood maltreatment and neuroticism by the corticotropin-releasing hormone receptor 1 gene. Association of CRHR1 and CRHR2 w...
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This is one of the SNPs reported by NutraHacker.
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Polymorphisms in inflammation-related genes are associated with susceptibility to major depression and antidepressant response. A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data. [PharmGKB:Curated This variant is associated with response to escitalopram and nortriptyline in a study of 760 adult patients with moderate-to-severe depression.]
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This is one of the SNPs reported by NutraHacker.
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Polymorphisms affecting gene transcription and mRNA processing in pharmacogenetic candidate genes: detection through allelic expression imbalance in human target tissues. Glucocorticoid receptor gene variant in the 3' untranslated region is associated with multiple measures of blood pressure. Cohort profile: risk patterns and processes for psychopathology emerging during adolescence: the ROOTS project. A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data. Glucocorticoid receptor gene haplotype structure and steroid therapy outcome in IBD patients. Association of FKBP5 gene haplotypes with completed suicide in the Japanese population. Glucocorticoid receptor polymorphism is associated with lithium response in bipolar patients.
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This is one of the SNPs reported by NutraHacker.
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Associated with insulin resistance in men Associated with bone mineral density and thus osteoporosis in a Chinese population. A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data.
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Associated with bone mineral density and thus osteoporosis in a Chinese population. A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data. Genetic modulation of neural response during working memory in healthy individuals: interaction of glucocorticoid receptor and dopaminergic genes.
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This is one of the SNPs reported by NutraHacker.
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower COMT enzymatic activity, therefore higher dopamine levels; lower pain threshold, enhanced vulnerability to stress, yet also more efficient at processing information under most conditions *rs4680(G) = Warrior. Val, less exploratory, higher COMT enzymatic activity, therefore lower dopamine levels; higher pain threshold, better stress resiliency, albeit with a modest reduction in executive cognition performance under most conditions Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis; summary at ) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compar...
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[PharmGKB:Curated On the basis of subjects' pain responsiveness, haplotypes involving rs6269 (A/G), rs4633 (C/T), rs4818 (C/G), and rs4680 (G/A) were designated as low (low pain sensitivity (LPS) haplotype; GCGG), average (average pain sensitivity (APS) haplotype; ATCA), or high (high pain sensitivity (HPS) haplotype; ACCG) pain sensitive.]
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This is one of the SNPs reported by NutraHacker.
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rs1208 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1208(G). [PharmGKB:Curated in vitro study; PK: 20-fold reduction in Vmax vs wild type] [OMIM:?]
normal
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rs1801394, also known as A66G or Ile22Met, is a SNP in the methionine synthase MTRR gene. This gene encodes one of the two enzymes involved in the production of methionine (the other is MTR). The protein encoded by an rs1801394 allele has a lower affinity for MTR () and is inconsistently associated with homocysteine level, although it is a risk factor for neural tube defects () and Down syndrome () in conditions of higher homocysteine. Based on a study of British patients with primary brain tumors, (1,005 glioma cases and 631 meningioma cases), rs1801394(G;G) individuals were at higher risk for meningioma (odds ratio 1.41, CI: 1.02-1.94). In general, genotypes associated with increased 5,10-methylenetetrahydrofolate levels are associated with elevated risk for these types of brain cancer. ...
40 snps
(hide) Pain
higher risk for endometrial cancer
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rs4633 is a variant at codon 62 of the COMT gene, however, it does not change the amino acid sequence of the COMT protein. In a study of 150 (Caucasian) cases of endometrial cancer, a significant increase in rs4633(T;T) genotype was observed in patients compared to controls (OR = 2.39, CI: 1.31-4.37, p = 0.004). Furthemore, the frequency of the C-G haplotype of rs4633-rs4680 was significantly higher in controls (p < 0.0001) than in patients. This correlated with lower expression levels of the COMT protein in carriers of these alleles. pubmed 1180576 Schizophrenia Susceptibility Genetic basis for individual variations in pain perception and the development of a chronic pain condition [PharmGKB:Curated On the basis of subjects' pain responsiveness, haplotypes involving rs6269 (A/G), rs46...
Magnitude: 1.7
possible low pain sensitivity
suggests you may be able to tolerate more pain than most people. However phased data may be necessary to increase certainty. See also gs232 gs233 gs234 gs235
possible high pain sensitivity
suggests you may be able to tolerate less pain than most people. However phased data may be necessary to increase certainty. See also gs232 gs233 gs234 gs235
Frequency: 45.1%
References:2
References:2
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study of acute post-surgical pain in humans. (Initial Sample Size: 60 females, 52 males; Replication Sample Size: NR); (Region: 11q23.3; Reported Gene(s): NR; Risk Allele: rs17122021-?); (p-value= 0.0000007).This variant is associated with Pain.] [GWAS:Pain]
slightly less drug dependence, decreased effectiveness of analgesics
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Genome-wide association study identifies a potent locus associated with human opioid sensitivity rs2952768(C) was associated with more analgesic requirements ... exhibited less vulnerability to severe methamphetamine or alcohol dependence, fewer eating disorders, and a lower ‘Reward Dependence’ score on a personality questionnaire. The (C;C) genotype was significantly associated with the elevated expression of a neighboring gene, CREB. SNPs in this locus are the most potent genetic factors associated with human opioid sensitivity known to date, affecting both the efficacy of opioid analgesics and liability to severe substance dependence. Our findings provide valuable information for the personalized treatment of pain and drug dependence. [GWAS:Opioid sensitivity]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study of acute post-surgical pain in humans. (Initial Sample Size: 60 females, 52 males; Replication Sample Size: NR); (Region: 1p21.3; Reported Gene(s): NR; Risk Allele: rs6693882-?); (p-value= 0.000002).This variant is associated with Pain.] [GWAS:Pain]
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower COMT enzymatic activity, therefore higher dopamine levels; lower pain threshold, enhanced vulnerability to stress, yet also more efficient at processing information under most conditions *rs4680(G) = Warrior. Val, less exploratory, higher COMT enzymatic activity, therefore lower dopamine levels; higher pain threshold, better stress resiliency, albeit with a modest reduction in executive cognition performance under most conditions Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis; summary at ) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compar...
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[PharmGKB:Curated On the basis of subjects' pain responsiveness, haplotypes involving rs6269 (A/G), rs4633 (C/T), rs4818 (C/G), and rs4680 (G/A) were designated as low (low pain sensitivity (LPS) haplotype; GCGG), average (average pain sensitivity (APS) haplotype; ATCA), or high (high pain sensitivity (HPS) haplotype; ACCG) pain sensitive.]
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Seems to play a role in the brain This is a synonymous change. it does not affect the amino acid. [PharmGKB:Curated On the basis of subjects' pain responsiveness, haplotypes involving rs6269 (A/G), rs4633 (C/T), rs4818 (C/G), and rs4680 (G/A) were designated as low (low pain sensitivity (LPS) haplotype; GCGG), average (average pain sensitivity (APS) haplotype; ATCA), or high (high pain sensitivity (HPS) haplotype; ACCG) pain sensitive.] [OMIM:CATECHOL-O-METHYLTRANSFERASE; COMT]
Magnitude: 0.1
normal pain sensitivity
You probably experience typical sensitivity to pain according to See also gs232, gs234, and gs235
Normal perception of pain
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rs6746030 is a SNP in the sodium channel Nav1.7 SCN9A gene. In five cohorts tested, totaling 1,277 individuals, the rarer rs6746030(A) allele was associated with increased pain (p=0.0001).
3 genosets 8 snps
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Lack of empathy? You have a SNP in the oxytocin receptor which may make you less empathetic than most people. When under stress you may have more difficulty recognizing the emotional state of others which impacts loneliness, parenting, and socializing skills. Some studies have suggested that the A;G genotype is associated with an intermediate level of empathy (compared to the G;G and A;A genotypes), although most report that A;G and A;A individuals have similar levels of empathy and stress handling capabilities.
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rs53576 is a silent G to A change in the oxytocin receptor (OXTR) gene. Studies have demonstrated that individuals with the G allele are more empathetic, feel less lonely, employ more sensitive parenting techniques, and have lower rates of autism (discussed in ) The blog Not Exactly Rocket Science discusses that Americans with (G;G) tend to be more sensitive parents, more empathetic and less lonely than those with an ‘A’. In a Korean population people with (G;G) were less likely to seek support from their peers. Culture, distress, and oxytocin receptor polymorphism (OXTR) interact to influence emotional support seeking. Oxytocin receptor genetic variation relates to empathy and stress reactivity in humans. In brief, people with the G;G genotype were better able to discern the e...
Normal risk of sexual dysfunction when taking SSRI Antidepressants.
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rs6311 (-1438A>G / A-1438G or -1438G>A / G-1438A) is a SNP located upstream (and within the promoter region of) HTR2A. Multiple Regulatory Variants Modulate Expression of 5-Hydroxytryptamine 2A Receptors in Human Cortex. The minor A allele of rs6311 reduces expression of a previously unannotated extension of the 5' untranslated region of HTR2A mRNA. rs6311 together with rs6314 have a modest effect on depression severity, when examined in the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study. Three (rs643627-rs594242-rs6311: A-C-T), two (rs594242-rs6311: C-T) and a single functional (rs6311: T) marker were protective against suicidal behavior. The complementary markers (rs594242-rs6311: G-C and rs6311: C) were associated with increased risk for non-violent and impu...
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rs1800544 (C-1291G) is a SNP located in the promoter region of ADRA2A (adrenergic receptor alpha 2A). GG genotype carriers had significantly higher consumption of sweet food products (Estonian Children Personality Behavior and Health Study subset, n = 419) GG genotype carriers had significantly higher scores on an assessment of depression, and significantly lower scores on morality and orderliness compared to CC carriers. girls with CC and CG genotypes scored higher than boys with the same genotypes on an assessment of extraversion. boys with GG genotypes, however, scored higher than girls with GG genotypes. GG genotype assoc. w/ higher scores of inattention Food Preference [OMIM:ALPHA-2A-ADRENERGIC RECEPTOR; ADRA2A]
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Our findings suggest an influence of the gene in the neural substrate mediating sensorimotor gating and working memory, especially when combined with high anxiety. Genetic associations with schizophrenia: meta-analyses of 12 candidate genes. The neurobiology of D-amino acid oxidase and its involvement in schizophrenia. Persistence criteria for susceptibility genes for schizophrenia: a discussion from an evolutionary viewpoint.
higher risk for RA
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rs6313, also known as T102C, is part of a 4-SNP haplotype in the serotonin 2A receptor gene HTR2A that has been associated with rheumatoid arthritis in a study of 1800 European patients. The risk allele is rs6313(C). The overall risk for the haplotype CTCC of SNPs rs6311-rs1328674-rs6313-rs6314 is 1.68 (CI: 1.20 - 2.34, p = 0.02). Note: the orientation of rs1328674 in dbSNP is opposite that cited by this publication; therefore, with respect to dbSNP, the haplotype of risk as cited above is CACC rather than CTCC. see also gs108 and gs226 Polymorphisms in the serotonin receptor gene HTR2A are associated with quantitative traits in panic disorder. [PharmGKB:Curated Risk or phenotype-associated allele (s): T/T. Phenotype: Patients, with a diagnosis of probable Alzheimer's disease, carryi...
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[PharmGKB:Non-Curated GWAS results: Genome-wide association scan for five major dimensions of personality. (Initial Sample Size: 3,972 individuals; Replication Sample Size: 3,903 individuals); (Region: 19q13.31; Reported Gene(s): ZNF180; Risk Allele: rs644148-G); (p-value= 0.0000009).This variant is associated with Personality dimensions(openness).] [GWAS:Personality dimensions]
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The G allele of SNAP25 gene SNP rs362584 was associated with increased neurotic traits (combined p value = 0.0000522) in a group of 3972 Sardinians, and two smaller replicative samples from the USA and Netherlands (the replicative samples were not significant by themselves, with the Netherlands sample showing considerably less of a trend).full paper in pdf
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[GWAS:Personality dimensions]
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The A allele of the CLOCK gene SNP rs6832769 was associated with lessened agreeableness (p = 0.00000871) in a group of 3972 Sardinians. The effect remained significant in the replicative American sample, but failed to achieve significance in the Norwegian sample and third sample (though the combined p value remained significant at 0.000865). full paper in pdf [PharmGKB:Non-Curated GWAS results: Genome-wide association scan for five major dimensions of personality. (Initial Sample Size: 3,972 individuals; Replication Sample Size: 3,903 individuals); (Region: 4q12; Reported Gene(s): CLOCK; Risk Allele: rs6832769-A); (p-value= 0.000002).This variant is associated with Personality dimensions.]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association scan for five major dimensions of personality. (Initial Sample Size: 3,972 individuals; Replication Sample Size: 3,903 individuals); (Region: 2p22.1; Reported Gene(s): THUMPD2; Risk Allele: rs2540226-T); (p-value= 0.000003).This variant is associated with Personality dimensions.] [GWAS:Personality dimensions]
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[GWAS:Personality dimensions]
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[GWAS:Personality dimensions]
normal
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rs1611115 (C-1021T) is a SNP near the dopamine beta-hydroxylase (DBH) gene. per OMIM, the T allele is associated with lower DBH expression in plasma (16 of TT genotype had DBH activity of 4.1, 46 of CT genotype had DBH activity of 25.2, and 112 of CC genotype had DBH activity of 48.1 nmol/min/ml) Association tests related to affective disorders such as ADHD were performed using four independent samples, healthy volunteers (N = 387), patients with affective disorders (N = 182), adult attention deficit hyperactivity disorder (ADHD) patients (N = 407), and patients with personality disorders (N = 637). Personality disorder patients carrying the DBH TT genotype exhibited higher neuroticism and novelty seeking scores as compared to individuals with the (C;C) or (C;T) genotype. Analyses on the l...
Frequency: 38.5%
References:1
References:1
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[GWAS:Personality dimensions]
normal; increased agreeableness (?)
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rs1800759 is a SNP in the promoter (regulatory region) of the alcohol dehydrogenase 4 (ADH4) gene. In a study of 500+ patients with either alcohol dependence or drug dependence, rs1800759 was the most significant ADH4 SNP to be associated (in a recessive manner) with increased risk for either condition, at least in Caucasians. In another study, a five-factor model of personality in 243 subjects with substance dependence (175 European Americans [EAs] and 68 African Americans [AAs]), along with 296 healthy control subjects (256 EAs and 40 AAs), was conducted in association with an ADH4 SNP survey. rs1800759(A) alleles and (A;A) genotypes A/A were significantly associated with agreeableness scores.
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[GWAS:Personality dimensions]
Frequency: 10.0%
References:1
References:1
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[GWAS:Personality]
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower COMT enzymatic activity, therefore higher dopamine levels; lower pain threshold, enhanced vulnerability to stress, yet also more efficient at processing information under most conditions *rs4680(G) = Warrior. Val, less exploratory, higher COMT enzymatic activity, therefore lower dopamine levels; higher pain threshold, better stress resiliency, albeit with a modest reduction in executive cognition performance under most conditions Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis; summary at ) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compar...
18 snps
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poorer metabolizer of several popular medicines; patients prescribed Plavix get less benefit, and have higher risk for adverse cardiovascular events
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rs4244285 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*2 variant. This variant is the most common reason for poor metabolism of compounds like mephenytoin (an anti-convulsant), some antidepressants, the anti-platelet drug Plavix, and some drugs used for ulcer conditions of various types. The risk allele is rs4244285(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (trade name Prevacid). In Caucasians, SNPs in CYP2C19 are relatively rare (in contrast to SNPs in CYP2D6), but SNPs in this gene are common in Asians. Ulcer treatment with omeprazole to reduce Helicobacter pyl...
Increased risk of hearing loss 15.2x risk of Age Related Hearing Impairment(ARHI), also known as presbycusis. This applies to the European and Turkish, but not Finnish populations.
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rs1799930 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. Also known as G590A. The risk allele for this SNP is rs1799930(A). [PharmGKB:Curated in vitro study; PK: 22-fold reduction in Vmax vs wild type] [OMIM:?]
Carrier of one CYP1A2*1F allele; Slow Caffeine Metabolizer. One copy of the slow caffeine metaboliser SNP, and one copy of the fast version. This makes you more strongly affected by drinking coffee, as caffeine is broken down slower in the liver. Supposedly this increases the risk of heart attacks, although other studies show caffeine is generally good for the heart. It also makes caffeine more effective at preventing Breast Cancer, Alzheimer's Disease, and Parkinson's disease. Too much caffeine will shrink your breasts.
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rs762551, also known as -164A>C or -163C>A, is a SNP encoding the CYP1A2*1F allele of the CYP1A2 gene. For historic reasons, the rs762551(C) allele is considered the wild-type, even though it is the rarer allele in most populations. The rs762551(A) allele is the 'fast metabolizer' allele known as CYP1A2*1F; the (C) allele is by comparison a slower metabolizer of certain substrates (including caffeine). In terms of genotypes, only rs762551(A;A) individuals are considered fast metabolizers. Individuals who are rs762551(A;C) heterozygotes or rs762551(C;C) homozygotes are both considered slow metabolizers. The CYP1A2 gene encodes a member of the cytochrome p450 family of proteins, which metabolize nutrients and drugs. One well known substrate of CYP1A2 is caffeine; individuals who are ca...
1.6x risk for ICP
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rs3740066, a SNP in the ABCC2 gene, is reported to be associated with a higher risk of developing intrahepatic cholestasis of pregnancy (ICP) based on a study of ~70 Argentinian patients. ICP is associated with increased fetal risks such as premature birth or intrauterine death. The risk allele is rs3740066(A), and the odds ratio for homozygous rs3740066(A;A) mothers is 4.44 (CI: 1.83 - 10.78), and for heterozygous mothers 1.65 (CI: 0.76 - 3.64), compared to rs3740066(G;G) mothers. [PharmGKB:Curated The AUCs of irinotecan, SN-38, SN-38 glucuronide, and APC are influenced by rs3740066, rs2306283, rs35605, rs10276036, and rs717620 .]
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[PharmGKB:Curated Risk or phenotype-associated allele: SLCO1B3: T334. Phenotype: The metabolic ratio of glucuronidated mycophenolic acid (MPAG) to mycophenolic acid (MPA) showed a very significant decrease in carriers of the SLCO1B3 T334 allele (p = 0.0001). Carriers of at least one SLCO1B3 T334 allele (n = 22) had a 1.42-fold higher (p = 0.0003) MPA AUC(0-12 hours) and a 1.38-fold higher (p = 0.0010) Cmax as compared with carriers of the 334GG genotype (n = 48). Patients carrying 334 TT or TC genotypes (n = 22) had significantly higher MPA AUC(4-9 hours) than patients carrying the CC genotype (n = 48; p = 0.0027). However, they also had higher AUC(0-4 h) (p = 0.0008), resulting in an unchanged AUC(4-9 h)/AUC(0-9 h) ratio (p = 0.4945). In the subgroups of patients cotreated with sirolimus ...
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[PharmGKB:Curated Risk or phenotype-associated allele: SCLO1B3 haplotype formed by 112Ser>Ala (rs4149117, 334T>G) and 223Met>Ile (rs7311358, 699G>A). Phenotype: HEK293 cells transiently expressing the SCLO1B3 334G-699A haplotype or reference haplotype were incubated in the presence of increasing concentrations of mycophenolic acid phenyl-glucuronide (MPAG) for 10 min. The uptake of MPAG according to the SCLO1B3 334G-699A haplotype was markedly lower than in cells expressing the reference sequence 334T-669G. Type of association: GN; FA; PK]
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rs2306283 (Asn130Asp/N130D, A388G/388A>G) is a SNP within SLCO1B1 (Solute carrier organic anion transporter family member 1B1). A G at this location denotes the SLCO1B1*1B allele. among 8 healthy volunteers with *1B/*1B genotypes and 16 with the *1A/*1A genotype, *1B/*1B genotype associated with reduced plasma concentrations of repaglinide (but not nateglinide) consistent with increased hepatic uptake by SLCO1B1 (but w/ limited effects on nateglinide pharmacokinetics) news rs2306283 influences statin-related myopathy risk Genotyping panel for assessing response to cancer chemotherapy. Common variants in the SLCO1B3 locus are associated with bilirubin levels and unconjugated hyperbilirubinemia. Pazopanib-induced hyperbilirubinemia is associated with Gilbert's syndrome UGT1A1 polymorphism...
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Pharmacokinetics of efavirenz when co-administered with rifampin in TB/HIV co-infected patients: pharmacogenetic effect of CYP2B6 variation. The pharmacokinetics and pharmacogenomics of efavirenz and lopinavir/ritonavir in HIV-infected persons requiring hemodialysis. Polymorphisms of drug-metabolizing enzymes (GST, CYP2B6 and CYP3A) affect the pharmacokinetics of thiotepa and tepa. The impact of cytokines on the expression of drug transporters, cytochrome P450 enzymes and chemokine receptors in human PBMC. Associations between CYP2B6 polymorphisms and pharmacokinetics after a single dose of nevirapine or efavirenz in African americans. CYP2B6 (c.516G-->T) and CYP2A6 (*9B and/or *17) polymorphisms are independent predictors of efavirenz plasma concentrations in HIV-infected patients. CYP...
Magnitude: 1
References:4
References:4
Reduced CYP2A6 metabolism; impaired nicotine metabolism?
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rs28399433, also known as -47A>C, is a SNP in the CYP2A6 gene. CYP2B6 (c.516G-->T) and CYP2A6 (*9B and/or *17) polymorphisms are independent predictors of efavirenz plasma concentrations in HIV-infected patients. CYP2B6 variants and plasma efavirenz concentrations during antiretroviral therapy in Port-au-Prince, Haiti. [PharmGKB:In-Depth This variant results in decreased enzyme expression and activity, which affects nicotine and coumarin metabolism; part of the CYP2A6*9 haplotype.]
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[PharmGKB:Non-Curated PEPT2*1 (350L-409P-509R) showed lower K m for glycyl-sarcosine as compared with PEPT2*2 (350F- 409S-509K) in transfected cells.]
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[PharmGKB:Non-Curated PEPT2*1 (350L-409P-509R) showed lower K m for glycyl-sarcosine as compared with PEPT2*2 (350F- 409S-509K) in transfected cells.]
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[PharmGKB:Non-Curated PEPT2*1 (350L-409P-509R) showed lower K m for glycyl-sarcosine as compared with PEPT2*2 (350F- 409S-509K) in transfected cells.]
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[PharmGKB:Non-Curated Increased metformin uptake in transfected cells] [GWAS:Blood metabolite levels]
increased risk of cannabis dependence, lower (normal) cancer risk '''Association between ABCB1 C3435T polymorphism and increased risk of cannabis dependence.''' (2009). Patients with cannabis dependence (n=40) had a significantly higher 3435C allele frequency (62.5% versus 43.8% respectively, P=0.017) and CC genotype (50% versus 20%, P=0.005, OR=4.00 [1.50-10.60). The CC genotype was independently associated with cannabis dependence. This is the first time a significant specific genetic marker has been shown in cannabis dependence. ABCB1 polymorphisms may alter Delta9THC distribution, its psychoactive effects and individual vulnerability to dependence.
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rs1045642, also known as C3435T, is a SNP located in the ABCB1 gene. It is often studied in conjunction with rs2032582. C3435T has been mentioned by: * A 'Silent' Polymorphism in the MDR1 Gene Changes Substrate Specificity (for example, to verapamil) * (R)-lansoprazole (Prevacid) concentrations are significantly increased in CYP2C19 extensive metabolizers with ABCB1 C3435T C allele. * In a Korean population, plasma concentrations of fexofenadine (Allegra) were 17% lower in 2677AA/3435CC subjects and 47% higher in the 2677TT/3435TT subjects compared to 2677GG/3435CC subjects. * In contrast, in this study no association was observed between the C3435T polymorphism and fexofenadine plasma or urine concentrations in a German Caucasian population. * A meta-analysis including 9 case-control stud...
normal. better response to atorvastatin. greater severity of delusions in male schizophrenics. '''Association study between the MDR1 gene and clinical characteristics in schizophrenia.''' (2014). Male schizophrenic carriers of the G allele of variant rs2032582 exhibit greater severity of delusions.
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rs2032582, also known as G2677T, is a nonsynonymous SNP located in exon 21 of the ABCB1 gene. G2677 is also known as Ala893Thr. It is often studied in conjunction with rs1045642. The rs2032582(T) variant allele yields a 2.6 fold higher risk of developing lung cancer, and in particular, the type of lung cancer called squamous cell carcinoma (CI 1.7-4.0, P < .001). There appears to be little gene dosage effect, since homozygous rs2032582(T;T) carriers shoulder almost all the risk (odds ratio 6.75 compared to (A;A) homozygotes, CI 3.0-15.2). This risk is also independent of an individual's history of smoking. A study of 98 methadone-maintaining patients concluded that the higher (>150 mg/day) and lower (< or =150 mg/day) methadone dose groups differed significantly in their rs1128503...
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[PharmGKB:Curated Alleles positive for this variant are designated CYP2C8*4. In in vitro experiments, the paclitaxel 6 alpha-hydroxylase acivity associated with CYP2C8*4 appeared lower than the wildtpe but the difference was not significant.]
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[PharmGKB:Curated N=24 Korean; PK: UGT2B15*2/*2 group vs UGT215*1/*1 showed 0.58 lower systemic clearance of lorazepam; p less than 0.001] [OMIM:URIDINE DIPHOSPHATE GLYCOSYLTRANSFERASE 2 FAMILY, MEMBER B28; UGT2B28]
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The (C;C) genotype is linked to reduced UGT1A1 activity, and increased Bilirubin, except in people of African origin for whom the T allele is a risk factor for breast cancer. [Genetic polymorphisms of MPO, NQO1, GSTP1, UGT1A6 associated with susceptibility of chronic benzene poisoning]. The influence of metabolic gene polymorphisms on urinary 1-hydroxypyrene concentrations in Chinese coke oven workers. Low-penetrance alleles predisposing to sporadic colorectal cancers: a French case-controlled genetic association study. [Relationship between genetic polymorphisms of phase I and phase II metabolizing enzymes and DNA damage of workers exposed to vinyl chloride monomer]. Serum bilirubin levels on ICU admission are associated with ARDS development and mortality in sepsis. Pazopanib-induced hyp...
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rs1801030 (Met223Val) is a snp within SULT1A1 (Sulfotransferase 1A1) and defines the SULT1A1*3 allele. [PharmGKB:In-Depth SULT1A1*3 is the second most common SULT1A1 SNP.]
References:5
carrier of one CYP2D6*41 allele
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rs28371725, also known as 2988G>A, is a SNP in the CYP2D6 gene. The rs28371725(A) allele defines the CYP2D6*41 variant, which has decreased activity. 23andMe also has SNP i4001476 at the same position. [PharmGKB:In-Depth This variant is part of the CYP2D6*41 IM haplotype. Plasma concentrations of metoprolol were shown to be were 4.9-fold higher in the PMs, with greater reductions in heart rate, diastolic blood pressure, and mean arterial pressure in PMs than in non-PMs.]
a common variant
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rs1080985 is a SNP near the CYP2D6 gene. Depending on the publication source, it may be called '-1584C/G' or '1496C>G' or the like. The wild type (normal) allele at this SNP is (C). The (G) variant indicates the presence of a non-wild type CYP2D6 variant, but it appears in many different variants so it can not be used to determine the presence of any particular variant. The rs1080985(G) allele defines the CYP2D6*2A variant, which has been reported to have relatively normal function yet in some cases may also lead to the intermediate metabolism phenotype. Please be careful when interpreting results for this SNP as it is in dbSNP and SNPedia in minus orientation where the risk allele is G, but test results are usually in plus orientation where the risk allele is C. This SNP has an ambiguo...
normal
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rs1128503 is a SNP in the transporter P-glycoprotein (P-gp) 170, encoded by the ABCB1 (also known as MDR1) gene. Methadone is a substrate of this protein, so variants may affect the efficacy and optimal dosage of this drug as used for treating opiate dependence. A study of 98 methadone-maintaining patients concluded that the higher (>150 mg/day) and lower (< or =150 mg/day) methadone dose groups differed significantly in their rs1128503 status (experiment-wise p = 0.0325). Furthermore, individuals with the 3-locus genotype pattern (T;T)-(T;T)-(T;T) for SNPs rs1045642, rs2032582 and rs1128503, respectively, had an approximately 5-fold chance of requiring the 'higher' methadone dose, while individuals heterozygous for these three SNPs have an approximately 3-fold chance of stabilizing ...
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rs1208 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1208(G). [PharmGKB:Curated in vitro study; PK: 20-fold reduction in Vmax vs wild type] [OMIM:?]
common in clinvar
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Technology to accelerate pangenomic scanning for unknown point mutations in exonic sequences: cycling temperature capillary electrophoresis (CTCE). Genetic variation in the one-carbon transfer pathway and ovarian cancer risk. Strong association of a common dihydropyrimidine dehydrogenase gene polymorphism with fluoropyrimidine-related toxicity in cancer patients. Genetic variation in TYMS in the one-carbon transfer pathway is associated with ovarian carcinoma types in the Ovarian Cancer Association Consortium. [PharmGKB:Curated Patients heterozygous for the C allele of this SNP exhibited increased incidence of medium-severe nausea and vomiting (as defined by WHO criteria) relative to those carrying only the T allele. The patient population consisted of individuals with gastric or colon ca...
26 snps
(hide) Pharma DMET
poorer metabolizer of several popular medicines; patients prescribed Plavix get less benefit, and have higher risk for adverse cardiovascular events
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rs4244285 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*2 variant. This variant is the most common reason for poor metabolism of compounds like mephenytoin (an anti-convulsant), some antidepressants, the anti-platelet drug Plavix, and some drugs used for ulcer conditions of various types. The risk allele is rs4244285(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (trade name Prevacid). In Caucasians, SNPs in CYP2C19 are relatively rare (in contrast to SNPs in CYP2D6), but SNPs in this gene are common in Asians. Ulcer treatment with omeprazole to reduce Helicobacter pyl...
watch out for high fat in diet
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rs1801282, also known as Pro12Ala, is a common SNP in the peroxisome proliferator-activated receptor PPARG gene. The more common (C) allele (in dbSNP orientation) encodes the 'Pro' amino acid at this SNP position. rs1801282 has been reported to be associated with metabolic syndrome, but other studies have not been able to replicate any strong or significant effect. The association between type-2 diabetes and SNP rs1801282 is mentioned as being replicated in rs1801282 and risk of cognitive decline in elders? Maybe with diabetes. A ten-year study of 679 male patients with symptomatic coronary artery disease found that rs1801282(G) carriers had a much lower (10 year) cardiovascular risk, with the hazard ratio estimated to be 0.10 (CI: 0.01-0.70, p = 0.02) for ischemic heart disease and 0.24 f...
Increased risk of hearing loss 15.2x risk of Age Related Hearing Impairment(ARHI), also known as presbycusis. This applies to the European and Turkish, but not Finnish populations.
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rs1799930 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. Also known as G590A. The risk allele for this SNP is rs1799930(A). [PharmGKB:Curated in vitro study; PK: 22-fold reduction in Vmax vs wild type] [OMIM:?]
Carrier of one CYP1A2*1F allele; Slow Caffeine Metabolizer. One copy of the slow caffeine metaboliser SNP, and one copy of the fast version. This makes you more strongly affected by drinking coffee, as caffeine is broken down slower in the liver. Supposedly this increases the risk of heart attacks, although other studies show caffeine is generally good for the heart. It also makes caffeine more effective at preventing Breast Cancer, Alzheimer's Disease, and Parkinson's disease. Too much caffeine will shrink your breasts.
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rs762551, also known as -164A>C or -163C>A, is a SNP encoding the CYP1A2*1F allele of the CYP1A2 gene. For historic reasons, the rs762551(C) allele is considered the wild-type, even though it is the rarer allele in most populations. The rs762551(A) allele is the 'fast metabolizer' allele known as CYP1A2*1F; the (C) allele is by comparison a slower metabolizer of certain substrates (including caffeine). In terms of genotypes, only rs762551(A;A) individuals are considered fast metabolizers. Individuals who are rs762551(A;C) heterozygotes or rs762551(C;C) homozygotes are both considered slow metabolizers. The CYP1A2 gene encodes a member of the cytochrome p450 family of proteins, which metabolize nutrients and drugs. One well known substrate of CYP1A2 is caffeine; individuals who are ca...
Magnitude: 2
Frequency: 43.1%
References:13
Frequency: 43.1%
References:13
CYP2C19*17 ultra fast metabolizer; drug metabolism effects; also 0.77x decreased breast cancer risk
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rs12248560(T) defines the CYP2C19*17 allele, an ultra fast metabolizer phenotype of the CYP2C19 gene. CYP2C19*17 is likely to lead to less effective drug treatment by, for example, proton pump inhibitors (such as omeprazole) and antidepressants. On the other hand, cancer patients who are CYP2C19*17 carriers are more likely to benefit from tamoxifen treatment, presumably because they break it down more rapidly into the antiestrogenic metabolites endoxifen and 4-hydroxytamoxifen. A study of 1,000+ breast cancer patients showed a 0.77x decreased risk of breast cancer for carriers of a CYP2C19*17 allele (CI: 0.65-0.93, p = 0.005). Analysis of a subgroup of such carriers who were using hormone therapy for ten years or longer showed an even stronger effect (odds ratio 0.57, CI: 0.39-0.83, p = 0....
Higher levels of serum bilirubin, associated with lower risk for coronary artery disease
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rs887829 is a SNP in the UGT1A1 gene. The minor allele of this SNP has been reported to be associated with higher levels of serum bilirubin, which has an inverse correlation with coronary artery disease. . This study of 2,000+ patients reports a recessive protective effect against coronary artery disease for the minor allele, with an age-adjusted odds ratio of 0.24 (CI: 0.10-0.60, p=0.0014). [PharmGKB:Curated This variant is in the promoter region of UGT1A1 and associated with serum bilirubin levels and hyperbilirubinemia in a genome wide association scan from 4300 Sardinian individuals.] [GWAS:Bilirubin levels]
2.1x increased risk of Crohn's disease
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rs1050152, a SNP in the SLC22A4 gene known as L503F, has been associated with an autoimmune disease, in this case, Crohn's disease, odds ratio = 2.1 (CI = 1.31–3.39, p = 0.002), based on a study of 203 cases and 200 controls. The risk allele is rs1050152(T). A nearby SNP (rs2631367) in the promoter region of the SLC22A5 gene defines a haplotype along with rs3792876, with odds ratio reported as similar for either SNP or the haplotype. Referring to the TC risk haplotype, the population risk attributable to heterozygotes was 19%, and for homozygous haplotype carriers, 27%. [PharmGKB:Non-Curated Higher gabapentin exposure and lower renal clearance/tubular secretion in individuals carrying this variant] [OMIM:?]
higher risk for endometrial cancer
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rs4633 is a variant at codon 62 of the COMT gene, however, it does not change the amino acid sequence of the COMT protein. In a study of 150 (Caucasian) cases of endometrial cancer, a significant increase in rs4633(T;T) genotype was observed in patients compared to controls (OR = 2.39, CI: 1.31-4.37, p = 0.004). Furthemore, the frequency of the C-G haplotype of rs4633-rs4680 was significantly higher in controls (p < 0.0001) than in patients. This correlated with lower expression levels of the COMT protein in carriers of these alleles. pubmed 1180576 Schizophrenia Susceptibility Genetic basis for individual variations in pain perception and the development of a chronic pain condition [PharmGKB:Curated On the basis of subjects' pain responsiveness, haplotypes involving rs6269 (A/G), rs46...
Carrier of at least one CYP2D6 variants (non-CYP2D6*1)
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rs1135840, also known as 4180G>C or S486T, is a SNP in the CYP2D6 gene. The wild type (normal) allele at this SNP is (G). The (C) variant indicates the presence of a non-wild type CYP2D6 variant, but it appears in many different variants so it can not be used to determine the presence of any particular variant. Please be careful when interpreting results for this SNP as it is in dbSNP and SNPedia in minus orientation where the risk allele is C, but test results are usually in plus orientation where the risk allele is G. This SNP has an ambiguous flip which can make this very confusing. Polymorphisms affecting gene transcription and mRNA processing in pharmacogenetic candidate genes: detection through allelic expression imbalance in human target tissues. [PharmGKB:Curated Risk or phenot...
normal oral/throat cancer risk; more frequent alcohol consumption
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A SNP in rs1229984 encodes a form of the alcohol dehydrogenase ADH1B gene that significantly reduces the clearance rate of alcohol from the liver. This SNP is also known as Arg48His, with the (G) allele corresponding to the Arg and the (A) to the His. Known in the literature as ADH2*2 or sometimes ADH1B*2, the allele with increased activity (meaning more rapid oxidation of ethanol to acetaldehyde) is His48, encoded by rs1229984(A). Individuals with one or especially two ADH2*2 alleles, ie genotypes rs1229984(A;G) or rs1229984(A;A) are more likely to find drinking unpleasant and have a somewhat reduced risk for alcoholism. A study of over 3,800 cases of 'upper aerodigestive' cancers (mouth/throat, voice box, and esophageal cancers) concluded that the rs1229984(A) allele (in dbSNP orientatio...
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[PharmGKB:Curated Risk or phenotype-associated allele: C Phenotype: The CHST3:rs4148943 C variant was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0001 Type of association: PD; CO]
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[PharmGKB:Curated Risk or phenotype-associated allele: C Phenotype: The CHST3:rs4148945 C variant was associated with positive clincial response (partial or complete response) to treatment and toxicity to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.011 (response); p = 0.010 (TOX) Type of association: PD; CO; TOX]
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[PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: The CHST3:rs4148950 A variant was associated with positive clincial response (partial or complete response) to treatment and toxicity to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s):p = 0.024 (response); p = 0.006 (TOX) Type of association: PD; CO; TOX]
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[PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: The CHST3:rs1871450 A variant was associated with positive clincial response (partial or complete response) to treatment and toxicity to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.048 (response); p = 0.006 (TOX) Type of association: PD; CO; TOX]
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[PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: The CHST3:rs730720 A variant was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0034 Type of association: PD; CO]
1.6x risk for ICP
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rs3740066, a SNP in the ABCC2 gene, is reported to be associated with a higher risk of developing intrahepatic cholestasis of pregnancy (ICP) based on a study of ~70 Argentinian patients. ICP is associated with increased fetal risks such as premature birth or intrauterine death. The risk allele is rs3740066(A), and the odds ratio for homozygous rs3740066(A;A) mothers is 4.44 (CI: 1.83 - 10.78), and for heterozygous mothers 1.65 (CI: 0.76 - 3.64), compared to rs3740066(G;G) mothers. [PharmGKB:Curated The AUCs of irinotecan, SN-38, SN-38 glucuronide, and APC are influenced by rs3740066, rs2306283, rs35605, rs10276036, and rs717620 .]
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CYP17 genotype is associated with short menstrual cycles, early oral contraceptive use and BRCA mutation status in young healthy women. Polymorphisms in the cytochrome P450 genes CYP1A2, CYP1B1, CYP3A4, CYP3A5, CYP11A1, CYP17A1, CYP19A1 and colorectal cancer risk. The rs743572 common variant in the promoter of CYP17A1 is not associated with prostate cancer risk or circulating hormonal levels. CYP17 genetic variation and risk of breast and prostate cancer from the National Cancer Institute Breast and Prostate Cancer Cohort Consortium (BPC3). Genetic polymorphisms in CYP17, CYP3A4, CYP19A1, SRD5A2, IGF-1, and IGFBP-3 and prostate cancer risk in African-American men: the Flint Men's Health Study. Genetic variation in CYP17 and endometrial cancer risk. Variants in hormone biosynthesis genes an...
carrier of one CYP2E1*7_-71G>T allele
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rs6413420 is a SNP in the CYP2E1 gene. The rs6413420(T) allele defines the CYP2E1*7_-71G>T variant.
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[GWAS:None]
Frequency: 54.0%
References:1
References:1
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[PharmGKB:Curated Risk or phenotype-associated allele: SLCO1B3: T334. Phenotype: The metabolic ratio of glucuronidated mycophenolic acid (MPAG) to mycophenolic acid (MPA) showed a very significant decrease in carriers of the SLCO1B3 T334 allele (p = 0.0001). Carriers of at least one SLCO1B3 T334 allele (n = 22) had a 1.42-fold higher (p = 0.0003) MPA AUC(0-12 hours) and a 1.38-fold higher (p = 0.0010) Cmax as compared with carriers of the 334GG genotype (n = 48). Patients carrying 334 TT or TC genotypes (n = 22) had significantly higher MPA AUC(4-9 hours) than patients carrying the CC genotype (n = 48; p = 0.0027). However, they also had higher AUC(0-4 h) (p = 0.0008), resulting in an unchanged AUC(4-9 h)/AUC(0-9 h) ratio (p = 0.4945). In the subgroups of patients cotreated with sirolimus ...
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[PharmGKB:Curated Risk or phenotype-associated allele: SCLO1B3 haplotype formed by 112Ser>Ala (rs4149117, 334T>G) and 223Met>Ile (rs7311358, 699G>A). Phenotype: HEK293 cells transiently expressing the SCLO1B3 334G-699A haplotype or reference haplotype were incubated in the presence of increasing concentrations of mycophenolic acid phenyl-glucuronide (MPAG) for 10 min. The uptake of MPAG according to the SCLO1B3 334G-699A haplotype was markedly lower than in cells expressing the reference sequence 334T-669G. Type of association: GN; FA; PK]
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rs2306283 (Asn130Asp/N130D, A388G/388A>G) is a SNP within SLCO1B1 (Solute carrier organic anion transporter family member 1B1). A G at this location denotes the SLCO1B1*1B allele. among 8 healthy volunteers with *1B/*1B genotypes and 16 with the *1A/*1A genotype, *1B/*1B genotype associated with reduced plasma concentrations of repaglinide (but not nateglinide) consistent with increased hepatic uptake by SLCO1B1 (but w/ limited effects on nateglinide pharmacokinetics) news rs2306283 influences statin-related myopathy risk Genotyping panel for assessing response to cancer chemotherapy. Common variants in the SLCO1B3 locus are associated with bilirubin levels and unconjugated hyperbilirubinemia. Pazopanib-induced hyperbilirubinemia is associated with Gilbert's syndrome UGT1A1 polymorphism...
References:6
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[PharmGKB:Curated Subjects homozygous for this genotype showed decreased response to fluvastatin]
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rs4646(A) allele carriers with breast cancer being treated with letrozole are reported to do worse than rs4646(C;C) patients, based on a study of (only) 95 women. [PharmGKB:Curated A study in 67 patients with hormone receptor-positive metastatic breast cancer treated with letrozole, the presence of this SNP in the 3' untranslated region of the CYP19A1 gene is associated with improved treatment efficacy.]
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Mutation analysis and the correlation between genotype and phenotype of Arg778Leu mutation in chinese patients with Wilson disease.
None
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rs2108622 is a SNP in the cytochrome P450, family 4, subfamily F, polypeptide 2 CYP4F2 gene. In the males rs2108622(G) was significantly higher in cerebral infarction patients (P = 0.025) A study of Italian patients concluded that rs2108622(T;T) patients require 5.49 mg/day of warfarin versus 2.93 mg/day for (C;C) patients. Analysis of variance indicates that about 7% of mean weekly warfarin dose variance is explained by CYP4F2 genotype. A study of 370 Brazilian ('admixed') patients concludes that prospective CYP4F2 genotyping is of little value to these patients, presumably due to ethnic-based differences. [PharmGKB:Curated Risk or phenotype-associated allele: no allelic association. Phenotype: Improved pharmacogenetic algorithm-based warfarin dosing. Study size: 370. Study population/et...
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Pharmacokinetics of efavirenz when co-administered with rifampin in TB/HIV co-infected patients: pharmacogenetic effect of CYP2B6 variation. The pharmacokinetics and pharmacogenomics of efavirenz and lopinavir/ritonavir in HIV-infected persons requiring hemodialysis. Polymorphisms of drug-metabolizing enzymes (GST, CYP2B6 and CYP3A) affect the pharmacokinetics of thiotepa and tepa. The impact of cytokines on the expression of drug transporters, cytochrome P450 enzymes and chemokine receptors in human PBMC. Associations between CYP2B6 polymorphisms and pharmacokinetics after a single dose of nevirapine or efavirenz in African americans. CYP2B6 (c.516G-->T) and CYP2A6 (*9B and/or *17) polymorphisms are independent predictors of efavirenz plasma concentrations in HIV-infected patients. CYP...
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Associations between CYP2B6 polymorphisms and pharmacokinetics after a single dose of nevirapine or efavirenz in African americans. Univariate/multivariate genome-wide association scans using data from families and unrelated samples. CYP2B6 variants and plasma efavirenz concentrations during antiretroviral therapy in Port-au-Prince, Haiti. Tests of association for quantitative traits in nuclear families using principal components to correct for population stratification. Family-based bivariate association tests for quantitative traits. A comparative study of three methods for detecting association of quantitative traits in samples of related subjects. Family-based genome-wide association study for simulated data of Framingham Heart Study. The Genetic Analysis Workshop 16 Problem 3: simulat...
Magnitude: 1
References:4
References:4
Reduced CYP2A6 metabolism; impaired nicotine metabolism?
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rs28399433, also known as -47A>C, is a SNP in the CYP2A6 gene. CYP2B6 (c.516G-->T) and CYP2A6 (*9B and/or *17) polymorphisms are independent predictors of efavirenz plasma concentrations in HIV-infected patients. CYP2B6 variants and plasma efavirenz concentrations during antiretroviral therapy in Port-au-Prince, Haiti. [PharmGKB:In-Depth This variant results in decreased enzyme expression and activity, which affects nicotine and coumarin metabolism; part of the CYP2A6*9 haplotype.]
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rs2279343, also known as Lys262Arg, is a SNP within the CYP2B6 gene. variants including the Arg allele include CYP2B6*4, CYP2B6*6, and CYP2B6*7 Pharmacokinetics of efavirenz when co-administered with rifampin in TB/HIV co-infected patients: pharmacogenetic effect of CYP2B6 variation. Polymorphisms of drug-metabolizing enzymes (GST, CYP2B6 and CYP3A) affect the pharmacokinetics of thiotepa and tepa. Associations between CYP2B6 polymorphisms and pharmacokinetics after a single dose of nevirapine or efavirenz in African americans. CYP2B6 variants and plasma efavirenz concentrations during antiretroviral therapy in Port-au-Prince, Haiti. Cyclophosphamide-metabolizing enzyme polymorphisms and survival outcomes after adjuvant chemotherapy for node-positive breast cancer: a retrospective cohort s...
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[PharmGKB:In-Depth This variant is associated with myocardial infarction and hypertension.]
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[PharmGKB:Non-Curated PEPT2*1 (350L-409P-509R) showed lower K m for glycyl-sarcosine as compared with PEPT2*2 (350F- 409S-509K) in transfected cells.]
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[PharmGKB:Non-Curated PEPT2*1 (350L-409P-509R) showed lower K m for glycyl-sarcosine as compared with PEPT2*2 (350F- 409S-509K) in transfected cells.]
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[PharmGKB:Non-Curated PEPT2*1 (350L-409P-509R) showed lower K m for glycyl-sarcosine as compared with PEPT2*2 (350F- 409S-509K) in transfected cells.]
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[GWAS:Blood metabolite levels]
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rs1051740, also known as Tyr113His, is a SNP in the microsomal epoxide hydrolase EPHX1 gene. severe hypersensitivity syndrome, triggered by carbamazepine in the presence of a concomitant active human herpes virus (HHV) 6 and 7 infection with the allele HLA-A*3101 and rs1051740(C;C) [PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: In a logistic regression model adjusted for history of phenytoin use during the first trimester and maternal epilepsy, the maternal EPHX1 113 H (rs1051740 T/C) allele was associated with craniofacial abnormalities in the child. Study size: 157 pregnancies. Study population/ethnicity: phenytoin use during the first trimester and maternal epilepsy. metric(s): per rare allele OR: 2.43, 95% confidence interval (CI): 1.16-5.10, P=0.02. Type of asso...
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[PharmGKB:Non-Curated Increased metformin uptake in transfected cells] [GWAS:Blood metabolite levels]
increased risk of cannabis dependence, lower (normal) cancer risk '''Association between ABCB1 C3435T polymorphism and increased risk of cannabis dependence.''' (2009). Patients with cannabis dependence (n=40) had a significantly higher 3435C allele frequency (62.5% versus 43.8% respectively, P=0.017) and CC genotype (50% versus 20%, P=0.005, OR=4.00 [1.50-10.60). The CC genotype was independently associated with cannabis dependence. This is the first time a significant specific genetic marker has been shown in cannabis dependence. ABCB1 polymorphisms may alter Delta9THC distribution, its psychoactive effects and individual vulnerability to dependence.
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rs1045642, also known as C3435T, is a SNP located in the ABCB1 gene. It is often studied in conjunction with rs2032582. C3435T has been mentioned by: * A 'Silent' Polymorphism in the MDR1 Gene Changes Substrate Specificity (for example, to verapamil) * (R)-lansoprazole (Prevacid) concentrations are significantly increased in CYP2C19 extensive metabolizers with ABCB1 C3435T C allele. * In a Korean population, plasma concentrations of fexofenadine (Allegra) were 17% lower in 2677AA/3435CC subjects and 47% higher in the 2677TT/3435TT subjects compared to 2677GG/3435CC subjects. * In contrast, in this study no association was observed between the C3435T polymorphism and fexofenadine plasma or urine concentrations in a German Caucasian population. * A meta-analysis including 9 case-control stud...
normal. better response to atorvastatin. greater severity of delusions in male schizophrenics. '''Association study between the MDR1 gene and clinical characteristics in schizophrenia.''' (2014). Male schizophrenic carriers of the G allele of variant rs2032582 exhibit greater severity of delusions.
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rs2032582, also known as G2677T, is a nonsynonymous SNP located in exon 21 of the ABCB1 gene. G2677 is also known as Ala893Thr. It is often studied in conjunction with rs1045642. The rs2032582(T) variant allele yields a 2.6 fold higher risk of developing lung cancer, and in particular, the type of lung cancer called squamous cell carcinoma (CI 1.7-4.0, P < .001). There appears to be little gene dosage effect, since homozygous rs2032582(T;T) carriers shoulder almost all the risk (odds ratio 6.75 compared to (A;A) homozygotes, CI 3.0-15.2). This risk is also independent of an individual's history of smoking. A study of 98 methadone-maintaining patients concluded that the higher (>150 mg/day) and lower (< or =150 mg/day) methadone dose groups differed significantly in their rs1128503...
Frequency: 26.5%
References:3
References:3
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[PharmGKB:Non-Curated The AUCs of irinotecan, SN-38, SN-38 glucuronide, and APC are influenced by rs3740066, rs2306283, rs35605, rs10276036, and rs717620 .]
higher risk for heart disease, diabetic retinopathy
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The snp is suspected of being somewhat confused as an ambiguous flip, because the ReferenceAllele of T has a HapMap freq of 15% in CEU. Also notable is that dbSNP shows RefSNP Alleles: A/C/G/T, and other bits that don't quite fit. While the text below is still of use, it is likely that some of the conclusions are reversed. rs854560, also known as L55M, is a SNP in the PON1 gene. It codes for amino acid 55 (or 54, depending on the numbering) of the paraoxonase (PON) protein. Variants of this SNP affect levels of PON protein and mRNA and are correlated with Heart disease, aspects of Diabetes including diabetic retinopathy, and trait-anxiety scores. The apparently more favorable form, rs854560(T), encodes a methionine and lead to elevated levels of paraoxonase, which is generally a good thing...
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rs1041983, also known as C282T, is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The allele associated with slow NAT2 metabolization for this SNP is rs1041983(T). Genosets gs154 and gs156 evaluate predicated NAT2 metabolizer phenotype based on rs1041983 and rs1801280. [PharmGKB:Curated in vitro study; PK: 22-fold reduction in Vmax vs wild type]
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Linkage disequilibrium blocks, haplotype structure, and htSNPs of human CYP7A1 gene. Cholesterol 7alpha-hydrolase (CYP7A1) c.-278A>C promoter polymorphism in gallstone disease patients. CYP7A1 (-204 A>C; rs3808607 and -469 T>C; rs3824260) promoter polymorphisms and risk of gallbladder cancer in North Indian population. Promoter variant -204A > C of the cholesterol 7alpha-hydroxylase gene: association with response to plant sterols in humans and increased transcriptional activity in transfected HepG2 cells.
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[PharmGKB:Curated Alleles positive for this variant are designated CYP2C8*4. In in vitro experiments, the paclitaxel 6 alpha-hydroxylase acivity associated with CYP2C8*4 appeared lower than the wildtpe but the difference was not significant.]
carrier of one CYP2C19*2B allele
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The rs17878459(C) SNP defines the CYP2C19 allele known as CYP2C19*2B, or as E92D.
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[PharmGKB:Curated N=24 Korean; PK: UGT2B15*2/*2 group vs UGT215*1/*1 showed 0.58 lower systemic clearance of lorazepam; p less than 0.001] [OMIM:URIDINE DIPHOSPHATE GLYCOSYLTRANSFERASE 2 FAMILY, MEMBER B28; UGT2B28]
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rs7439366, also known as Y268H, is a SNP in the UGT2B7 gene encoding the 2B7 UDP-Glucuronosyltransferase, active primarily in the liver. The rs7439366(C) allele encodes a histidine (H) at amino acid 268, and the (T) allele encodes a tyrosine (Y). Most publications refer to the histidine as the wild-type (more common) allele. In a study of glucuronidation activity of human livers, rs7439366(T;T) individuals had 28% lower activity than rs7439366(C;C) individuals with respect to O-glucuronidation of tamoxifen metabolites 4-OH-tamoxifen and endoxifen. The authors suggest this may help explain interindividual variability (beyond CYP2D6 variation) in tamoxifen metabolism - and therefore the effectiveness of tamoxifen in reducing breast cancer recurrence. [PharmGKB:Curated Risk or phenotype-asso...
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[GWAS:HDL cholesterol]
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association of the rs7483 SNP with late-onset Alzheimer's disease
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[PharmGKB:Curated UGT1A7:-57T>G increases risk of anemia in irinotecan-treated patients.]
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The (C;C) genotype is linked to reduced UGT1A1 activity, and increased Bilirubin, except in people of African origin for whom the T allele is a risk factor for breast cancer. [Genetic polymorphisms of MPO, NQO1, GSTP1, UGT1A6 associated with susceptibility of chronic benzene poisoning]. The influence of metabolic gene polymorphisms on urinary 1-hydroxypyrene concentrations in Chinese coke oven workers. Low-penetrance alleles predisposing to sporadic colorectal cancers: a French case-controlled genetic association study. [Relationship between genetic polymorphisms of phase I and phase II metabolizing enzymes and DNA damage of workers exposed to vinyl chloride monomer]. Serum bilirubin levels on ICU admission are associated with ARDS development and mortality in sepsis. Pazopanib-induced hyp...
References:6
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Clinically relevant UGT1A10 variant. [PharmGKB:Curated *93 is a common variant of UGT1A1 in Caucasian and African-American populations. It is located in the Phenobarbital Response Enhancer Module (an upstream regulatory sequence) and may be important in predicting irinotecan response.]
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[PharmGKB:Curated Risk or phenotype-associated allele: None. Phenotype: Variants identified in a screen of 13 genes involved in the gemcitabine drug metabolic pathway. For the non-synonymous CDA:79A>C (K27Q) SNP, the C allele (27Gln) was at frequency 0.36 and 0.04 in Europeans and Africans, respectively. There was a significant difference between ethnic groups in genotype frequency distribution (p < 0.001) Study size: 180. Study population/ethnicity: Healthy, unrelated blood donors of European (n = 95) and African (n = 85) descent. Significance metric(s): p < 0.001. Type of association: GN.]
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The SULT1C2: rs1402467 G variant was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0083 Type of association: PD; CO]
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[PharmGKB:Curated Risk or phenotype-associated allele: T Phenotype: The SPG7:rs2292954 T variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0004 Type of association: CO; TOX]
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The SPG7:rs12960 G variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.004 Type of association: CO; TOX]
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[PharmGKB:Curated Risk or phenotype-associated allele: None. Phenotype: Variants identified in a screen of 13 genes involved in the gemcitabine drug metabolic pathway. For the non-synonymous SLC28A2:283A>C (R75S) SNP, the C (75Ser) allele was at frequency was 0.34 and 0.08 in Europeans and Africans, respectively. There was a significant difference between ethnic groups in genotype frequency distribution (p < 0.001). Study size: 187. Study population/ethnicity: Healthy, unrelated blood donors of European (n = 95) and African (n = 92) descent. Significance metric(s): p < 0.001. Type of association: GN.]
References:2
carrier of one CYP1A2*1D allele
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rs35694136, also known as -2467delT, is a SNP in the CYP1A2 gene. The rs35694136(-) allele defines the CYP1A2*1D variant.
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[PharmGKB:Non-Curated altered kinetics of gemcitabine in transfected cells]
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[PharmGKB:Curated Risk or phenotype-associated allele: None. Phenotype: Variants identified in a screen of 13 genes involved in the gemcitabine drug metabolic pathway. For the SLC28A1:1383C>T SNP, the T allele was at frequency was 0.08 and 0.05 in Europeans and Africans, respectively. There was no significant difference between ethnic groups in genotype frequency distribution (p > 0.05). Study size: 185. Study population/ethnicity: Healthy, unrelated blood donors of European (n = 91) and African (n = 94) descent. Significance metric(s): Not significant, p > 0.05. Type of association: GN.]
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[PharmGKB:Curated Risk or phenotype-associated allele: None. Phenotype: Variants identified in a screen of 13 genes involved in the gemcitabine drug metabolic pathway. For the non-synonymous SLC28A1:1576T>C (N521D) SNP, the C (521Asp) allele was at frequency was 0.47 and 0.00 in Europeans and Africans, respectively. There was a significant difference between ethnic groups in genotype frequency distribution (p < 0.001). Study size: 185. Study population/ethnicity: Healthy, unrelated blood donors of European (n = 94) and African (n = 91) descent. Significance metric(s): p < 0.001. Type of association: GN.]
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rs212090(A;T) (T;T) increased cancer susceptibility (OR, 1.37; 95% CI, 1.03-1.83)
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The ABCC6 rs2238472 G variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.006 Type of association: CO; TOX] [OMIM:PSEUDOXANTHOMA ELASTICUM]
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rs1801030 (Met223Val) is a snp within SULT1A1 (Sulfotransferase 1A1) and defines the SULT1A1*3 allele. [PharmGKB:In-Depth SULT1A1*3 is the second most common SULT1A1 SNP.]
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[PharmGKB:In-Depth May be associated with a higher warfarin dose phenotype]
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[PharmGKB:Curated This SNP is the tagging SNP for VKORC1*2.]
References:7
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[PharmGKB:Curated This SNP is the tagging SNP for VKORC1*4.]
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rs272893 and rs273900 are associated with Crohn's disease (OR 2.16; 95% CI 1.21-3.59 and OR 2.40; 95% CI 1.43-4.05)
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Identification of a haplotype block in the 5q31 cytokine gene cluster associated with the susceptibility to severe malaria.
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Polymorphisms affecting gene transcription and mRNA processing in pharmacogenetic candidate genes: detection through allelic expression imbalance in human target tissues. Glucocorticoid receptor gene variant in the 3' untranslated region is associated with multiple measures of blood pressure. Cohort profile: risk patterns and processes for psychopathology emerging during adolescence: the ROOTS project. A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data. Glucocorticoid receptor gene haplotype structure and steroid therapy outcome in IBD patients. Association of FKBP5 gene haplotypes with completed suicide in the Japanese population. Glucocorticoid receptor polymorphism is associated with lithium response in bipolar patients.
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The PPAR delta SNP rs7769719 A>G was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0055 Type of association: PD; CO]
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rs1053049, rs6902123, and rs2267668 in PPARD affect Lifestyle Intervention induced changes in overall adiposity, hepatic fat storage, and relative muscle mass. Our findings provide a mechanistic explanation for the involvement of these genetic variations in the development of insulin resistance and type-2 diabetes. [OMIM:PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR-GAMMA, COACTIVATOR 1, ALPHA;]
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The PPAR delta SNP rs6922548 A>G was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0011 Type of association: PD; CO]
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[PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: CBR3 11G>A variant was associated with lower doxorubicinol AUC, lower CBR3 expression in breast tumor tissue, greater tumor reduction, and greater percentage reduction of leukocyte and platelet counts at nadir. Study size: 101 Study population/ethnicity: Asian; patients with Breast Neoplasms; Chinese; Malay; Indian Significance metric(s): p = 0.009 (AUC); p = 0.001 (expression); p = 0.015 (tumor reduction); p = 0.03 (leukocyte and platelet counts). Type of association: PK; TOX]
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common trait being optimism [GWAS:Common traits (Other)]
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower COMT enzymatic activity, therefore higher dopamine levels; lower pain threshold, enhanced vulnerability to stress, yet also more efficient at processing information under most conditions *rs4680(G) = Warrior. Val, less exploratory, higher COMT enzymatic activity, therefore lower dopamine levels; higher pain threshold, better stress resiliency, albeit with a modest reduction in executive cognition performance under most conditions Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis; summary at ) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compar...
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The 1661G>C variation in CYP2D6. Involved in a number of decreased and non-functioning CYP2D6 variants. This SNP does not yet appear to be common in consumer tests.
References:5
carrier of one CYP2D6*41 allele
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rs28371725, also known as 2988G>A, is a SNP in the CYP2D6 gene. The rs28371725(A) allele defines the CYP2D6*41 variant, which has decreased activity. 23andMe also has SNP i4001476 at the same position. [PharmGKB:In-Depth This variant is part of the CYP2D6*41 IM haplotype. Plasma concentrations of metoprolol were shown to be were 4.9-fold higher in the PMs, with greater reductions in heart rate, diastolic blood pressure, and mean arterial pressure in PMs than in non-PMs.]
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[OMIM:?]
a common variant
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The wild type (normal) allele at this SNP is (G). The (A) variant indicates the presence of a non-wild type CYP2D6 variant, but it appears in many different variants so it can not be used to determine the presence of any particular variant. Inheriting a normal number of copies of this allele results in CYP2D6 function that is indistinguishable from wild-type (normal) activity. However, this variant has been seen present in higher copy numbers, and in these cases, can result in the ultrafast metabolizer phenotype . [PharmGKB:In-Depth Risk or phenotype-associated allele: T. Phenotype: The CYP2D6*2A haplotype was associated with lower incidence of breast cancer on tamoxifen compared to placebo in a prevention study. The CYP2D6*2A allele may be associated with increased efficacy of tamoxifen....
a common variant
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rs1080985 is a SNP near the CYP2D6 gene. Depending on the publication source, it may be called '-1584C/G' or '1496C>G' or the like. The wild type (normal) allele at this SNP is (C). The (G) variant indicates the presence of a non-wild type CYP2D6 variant, but it appears in many different variants so it can not be used to determine the presence of any particular variant. The rs1080985(G) allele defines the CYP2D6*2A variant, which has been reported to have relatively normal function yet in some cases may also lead to the intermediate metabolism phenotype. Please be careful when interpreting results for this SNP as it is in dbSNP and SNPedia in minus orientation where the risk allele is G, but test results are usually in plus orientation where the risk allele is C. This SNP has an ambiguo...
common
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rs1080983 is a SNP near the 5' end of the CYP2D6 gene. Little is known of the significance of either allele.
normal
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rs915909 is a SNP in the CYP2E1 gene. The rs915909(T) allele defines the CYP2E1_6498C>T(I321I) variant.
normal
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rs1128503 is a SNP in the transporter P-glycoprotein (P-gp) 170, encoded by the ABCB1 (also known as MDR1) gene. Methadone is a substrate of this protein, so variants may affect the efficacy and optimal dosage of this drug as used for treating opiate dependence. A study of 98 methadone-maintaining patients concluded that the higher (>150 mg/day) and lower (< or =150 mg/day) methadone dose groups differed significantly in their rs1128503 status (experiment-wise p = 0.0325). Furthermore, individuals with the 3-locus genotype pattern (T;T)-(T;T)-(T;T) for SNPs rs1045642, rs2032582 and rs1128503, respectively, had an approximately 5-fold chance of requiring the 'higher' methadone dose, while individuals heterozygous for these three SNPs have an approximately 3-fold chance of stabilizing ...
common in complete genomics
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[PharmGKB:Curated This variant is the defining SNP for CYP3A7*2 which has increased catalytic acitivity compared to wild type.]
normal
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The rs2740574(G) allele encodes a variant form of CYP3A4 known as CYP3A4*1B. rs2740574(G) alleles are associated with an ~10 fold higher risk of aggressive prostate cancer in African American males. [PMID 16414488, OMIM A pooled study (1,400+ samples) along with a replication study conducted by members of the Ovarian Cancer Association Consortium found a 2.5-2.8x increased risk for ovarian cancer] for rs2740574(G;G) individuals (CI: 1.2-6.5, p=0.017). The authors note that CYP3A4 encodes a key enzyme in estrogen metabolism and which may be linked to ovarian carcinogenesis. [PharmGKB:Curated Risk or phenotype-associated allele: CYP3A4*1B, rs2740574 G allele. Phenotype: CYP3A4*1B (rs2740574 G) allele carriers show a significantly increased risk for SCLC (OR = 2.25, p = 0.02), which showed a...
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rs1208 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1208(G). [PharmGKB:Curated in vitro study; PK: 20-fold reduction in Vmax vs wild type] [OMIM:?]
normal
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SNP rs283413, also known as G78stop or Gly78X, encodes a rare variant of the ADH1C gene that leads to a truncated alcohol dehydrogenase protein. These types of proteins are involved in detoxification and may be linked to neurodegenerative diseases. The rs283413(G) allele is the more common, encoding the amino acid glycine (Gly); the quite rare rs283413(T) allele encodes the variant stop codon (X). Originally identified in three Swedish patients with Parkinson's disease (PD), a study of ~1000 PD patients vs. ~1000 controls indicated an odds ratio for the risk allele of 3.25 (CI:1.31-8.05). [This risk is effectively for heterozygotes, since the risk allele is so rare that no homozygotes for it were observed.] In a study of 40 index cases, 10% were found to harbor the rs283413(T) risk allele....
common in clinvar
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Technology to accelerate pangenomic scanning for unknown point mutations in exonic sequences: cycling temperature capillary electrophoresis (CTCE). Genetic variation in the one-carbon transfer pathway and ovarian cancer risk. Strong association of a common dihydropyrimidine dehydrogenase gene polymorphism with fluoropyrimidine-related toxicity in cancer patients. Genetic variation in TYMS in the one-carbon transfer pathway is associated with ovarian carcinoma types in the Ovarian Cancer Association Consortium. [PharmGKB:Curated Patients heterozygous for the C allele of this SNP exhibited increased incidence of medium-severe nausea and vomiting (as defined by WHO criteria) relative to those carrying only the T allele. The patient population consisted of individuals with gastric or colon ca...
125 snps
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Magnitude: 3
Repute:Bad
References:173
Repute:Bad
References:173
~20-25% of such hepatitis C patients respond to treatment This is considered an unfavorable response genotype for hepatitis C patients considering the use of PEG-interferon-alpha containing therapeutic treatment. This basically means the odds of a successful response are lower than for patients with the rs12979860(C;C) genotype.
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rs12979860 is a SNP near the IL28B gene, encoding interferon-lambda-3 (IFN-lambda-3). Several studies now indicate that this SNP predicts hepatitis C treatment-induced viral clearance. It is associated with an approximately twofold change in response to pegylated interferon-alpha (PEG-IFN-alpha) plus ribavirin (RBV) treatment, both among patients of European ancestry (p = 1.06 x 10e-25) and African-Americans (p = 2.06 x 10e-3). These studies indicate that the virus was eradicated in ~80% of (C;C) patients, compared to only about 25% of those with (T;T), while (C;T) response was intermediate. FDA PGx mentions about rs12979860 with respect to Boceprevir, Simeprevir, Sofosbuvir, and Telaprevir 23andMe blog rs8099917(C) less likely to respond to Hepatitis C treatment. A functional SNP rs368234...
lower odds of responding to PEG-IFNalpha/RBV treatment Substantially lower odds of responding to PEG-IFNalpha/RBV treatment for hepatitis C.
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23andMe blog rs8099917(C) less likely to respond to Hepatitis C treatment. rs12979860(C;C) better able to become naturally Hepatitis C virus-free. rs12980275(A) usually corresponds to the rs12979860(C) [PharmGKB:Curated Risk or phenotype-associated allele: G. Phenotype: This variant is associated with null virological response (NVR) and sustained virologic response (SVR) in Janapese patients with hepatitis C virus infection treated with PEG-INF-alpha plus ribavirin. Study size: Initial sample:154; Replication Sample: 172. Study population/ethnicity: Japanese. Significance metric(s): P=3.11 x 10(-15) (NVR); P = 1.11 x 10(-27)(SVR). Type of association: GN; CO] [OMIM:INTERLEUKIN 28B; IL28B] [GWAS:Response to Hepatitis C treatment]
poorer metabolizer of several popular medicines; patients prescribed Plavix get less benefit, and have higher risk for adverse cardiovascular events
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rs4244285 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*2 variant. This variant is the most common reason for poor metabolism of compounds like mephenytoin (an anti-convulsant), some antidepressants, the anti-platelet drug Plavix, and some drugs used for ulcer conditions of various types. The risk allele is rs4244285(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (trade name Prevacid). In Caucasians, SNPs in CYP2C19 are relatively rare (in contrast to SNPs in CYP2D6), but SNPs in this gene are common in Asians. Ulcer treatment with omeprazole to reduce Helicobacter pyl...
homozygous for C677T of MTHFR = 10-20% efficiency in processing folic acid = high homocysteine, low B12 and folate levels This is the homozygous form of the C677T allele for the MTHFR gene. It is found in approximately * 15% of Hispanic Americans * 12% of Caucasian Americans * 12% of Japanese * 6% of Germans * 3% of Asians * 2% of African Americans * 1% of Sub-Saharan Africans Numerous health effects are associated with this variant. * Hyperhomocysteinemia and neurologic disorders: a review. (2014). A review. Certain genetic factors also cause elevated homocysteine levels, such as C667T substitution of the gene encoding methylenetetrahydrofolate reductase. Elevated homocysteine has been observed in several medical conditions, such as cardiovascular disorders, atherosclerosis, myocardial i...
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer ** renal cancer * cleft lip and cleft palate * coronary artery disease * dementia * depression * hyperhomocysteinemia * migraine * neural tube d...
watch out for high fat in diet
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rs1801282, also known as Pro12Ala, is a common SNP in the peroxisome proliferator-activated receptor PPARG gene. The more common (C) allele (in dbSNP orientation) encodes the 'Pro' amino acid at this SNP position. rs1801282 has been reported to be associated with metabolic syndrome, but other studies have not been able to replicate any strong or significant effect. The association between type-2 diabetes and SNP rs1801282 is mentioned as being replicated in rs1801282 and risk of cognitive decline in elders? Maybe with diabetes. A ten-year study of 679 male patients with symptomatic coronary artery disease found that rs1801282(G) carriers had a much lower (10 year) cardiovascular risk, with the hazard ratio estimated to be 0.10 (CI: 0.01-0.70, p = 0.02) for ischemic heart disease and 0.24 f...
One copy of H63D, carrier of hemochromatosis, likely unaffected unless also C282Y carrier. You are a carrier for rs1799945(G) H63D Hereditary hemochromatosis. You are unlikely to be affected unless also a carrier of rs1800562(A) C282Y, but others in your family may be. This is a treatable condition.
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rs1799945, also known as H63D or His63Asp, represents a SNP that accounts for a mild form of hereditary hemochromatosis (HH), an iron overload condition in which mutations of certain genes involved in iron metabolism disrupt the body’s ability to regulate uptake of iron, causing increased intestinal iron absorption. The most common form is caused by mutations in the HFE gene, which are inherited recessively. The gene for HH is closely linked to the HLA-A3 locus on the short arm of chromosome 6 . In 1996, HFE, a gene for HH, was found to have two missense mutations . A mutation at amino acid 282 (C282Y) was found to be homozygous in 83 percent of patients with HH. This is a point mutation from guanine to adenine, resulting in a missense mutation from cysteine to tyrosine. Such mutatio...
A1/A2: Bad at avoidance of errors. 0.5x lower OCD risk, 0.87x lower Tardive Diskinesia risk, higher ADHD risk. More Alcohol Dependence. Lower risk of Postoperative Nausea. Increased obesity. Bupropion is not effective. The DRD2 TaqIA A1/A2 version causes less dopamine receptors. Doesn't learn from mistakes well. Reduced response to errors and increased addictive behavior Men may have half the risk of Obsessive Compulsive Disorder but higher risk of ADHD. Women have lower Persistence. 0.87x reduced risk of Tardive Diskinesia when taking dopamine receptor antagonists. Slightly increased risk of alcoholism and smoking addiction. Slower recovery from traumatic brain injury. Lower risk of postoperative nausea within 6 hours of surgery. Bupropion (Wellbutrin, Budeprion, Prexaton, Elontril, Aple...
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rs1800497, a SNP also known as the TaqIA (or Taq1A) polymorphism of the dopamine D2 receptor DRD2 gene (even though it is actually located over 10,000bp downstream of the gene), gives rise to the DRD2*A1 allele. This allele (rs1800497(T)) is associated with a reduced number of dopamine binding sites in the brain . Reduced response to errors and increased addictive behavior It has been postulated to play a role in alcoholism, smoking, and certain neuropsychiatric disorders. The reduced number of dopamine binding sites may play a role in nicotine addiction by causing an 'understimulated' state that can be relieved by smoking (and/or use of other drugs). A wide variety of reports have been published over more than ten years either linking rs1800497 to aspects of nicotine use and smoking cessa...
Increased risk of hearing loss 15.2x risk of Age Related Hearing Impairment(ARHI), also known as presbycusis. This applies to the European and Turkish, but not Finnish populations.
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rs1799930 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. Also known as G590A. The risk allele for this SNP is rs1799930(A). [PharmGKB:Curated in vitro study; PK: 22-fold reduction in Vmax vs wild type] [OMIM:?]
Magnitude: 2.5
Repute:Bad
References:3
Repute:Bad
References:3
Avoid Plavix, higher risk for adverse cardiovascular events. Neighboring rs4244285 is a more reliable predictor, but this genotype is linked to being a poor metabolizer of several popular medicines; patients prescribed Plavix (Clopidogrel) have higher risk for adverse cardiovascular events.
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JAMA rs12777823 and rs4244285 implicated in platelet response to clopidogrel [PharmGKB:Curated A GWAS found this variant (rs12777823) was the most significantly associated SNP with clopidogrel response. This SNP was in strong linkage disequilibrium with 12 further SNPs within the CYP2C18-CYP2C19-CYP2C9-CYP2C8 cluster (rs12777823; rs10109204; rs2025445; rs1326837; rs717238; rs2860838; rs2860903; rs9332105; rs9332113; rs12572351; rs10509679; rs1934951; rs1934680) and also with the loss-of-function variant CYP2C19*2 (rs4244285). Further findings in this study showed that the CYP2C19*2 genotype accounted for most of all the initially found association with diminished platelet response to clopidogrel.]
1.3x risk of rheumatoid arthritis; 1.55x risk of SLE; 1.42x risk of Sjögren's syndrome; increased risk of type-1 diabetes; and increased risk of primary biliary cirrhosis.
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rs7574865, a SNP in the third intron of the STAT4 gene, has been reported in a large study of Swedes to be associated with both rheumatoid arthritis (RA) and lupus (SLE). Among other studies, it has been confirmed in a meta-analysis of 8 studies totaling 7,381 patients and over 10,000 controls from both European and Asian populations. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated the presence of a risk allele was 1.3 for rheumatoid arthritis and 1.55 for lupus (SLE). The paper states that, 'Homozygosity of the risk allele, as compared with absence of the allele, was associated with a more than doubled risk for lupus and a 60% increased risk for rheumatoid arthritis.' A study of 124 Caucasian patients with primary Sjögren's syndrome, an autoimmune dise...
2.5x risk for AMD; higher mortality among nonagenarians To minimize your risk of age related macular degeneration, consider a diet rich in vitamins C and E, lutein, zeaxanthin and the minerals zinc and copper, such as kale, spinach and broccoli. source
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rs1061170 is a SNP in the complement factor H CFH gene; it is also known as Tyr402His. The rs1061170(T) allele encodes the more common Tyr (Y), while the generally rarer rs1061170(C) encodes the His (H). This SNP has been associated primarily with age related macular degeneration, and to a lesser extent, with longevity. This research paper shows that CFH Y402H is the relevant mutation. A haplotype of rs1061170 rs3753394 rs800292 rs1329428 (TGTC) was found to confer a significantly increased likelihood of exudative AMD. rs1061170 (aka Y402H 1277 T>C) was not associated with exudative AMD. CFH variations appear to contribute to ARMD in Caucasians, but not in Japanese CFH variant rs1061170 Y402H is strongly associated with both dry and wet AMD rs1061170(C) alleles are significantly associa...
Associated with Alcohol Dependence; associated with nicotine dependence (female) Cannabinoid Receptor 1 Gene is Associated with Alcohol Dependence. Alcoholic patients with TGT haplotype (corresponding to rs6454674-rs1049353-rs806368 polymorphisms in this order) were less prone to have AD (p = 0.017). TGC haplotype were more likely to develop AD. Cannabinoid receptor 1 gene association with nicotine dependence. the associations were female specific. Haplotype 1-1-2 of markers rs2023239-rs12720071-rs806368(C) was associated with nicotine dependence and FTND score in the 2 samples (P < .001 and P = .009, respectively).
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risk of the development of substance dependence significantly increased with the number of 'G' alleles at rs6454674 and SNP8 (rs806368);T/T genotypes had significant interaction effects (p = .0003 for comorbid drug dependence (DD) and alcohol dependence (AD), .0002 for DD, and .007 for AD). SNP3 and SNP8 together exerted stronger genetic effects on SD (substance dependence) than either did individually. The peak delta values among all the markers were seen for SNP3 and SNP8 (rs806368) rs806368(C) together with rs1049353(A) or rs1049353(G) make up a haplotype associated with PTSD, with the C-A haplotype somewhat associated (p=0.04) with higher risk of PTSD and the C-G haplotype associated (p=0.01) with a lower risk of PTSD. Alcoholic patients with TGT haplotype (corresponding to rs6454674-r...
3.9x increased risk of wet ARMD age related macular degeneration
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rs1136287, also known as Met72Thr, is a SNP in the PEDF gene. Analysis of 86 Taiwanese Chinese patients with wet age related macular degeneration (ARMD) found the (T) allele to be more frequent in patients than in controls (50% vs 31%; p =.0005). The rs1136287(T;T) genotype was also more prevalent in patients than in controls (odds ratio 3.9, p = .0015).
1.32 x risk of rheumatoid arthritis. A common genetic variant at the TRAF1-C5 locus on chromosome 9 is associated with an increased risk of anti-CCP-positive rheumatoid arthritis. rs3761847, a SNP located between two genes associated with chronic inflammation (TRAF1 and C5), is associated with increased risk of anti CCP-positive rheumatoid arthritis. The risk allele is (G); the odds ratio reported is 1.32 (95% confidence interval, 1.23 to 1.42; P=4x10-14) .
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rs3761847, a SNP located between two genes associated with chronic inflammation (TRAF1 and C5), is associated with increased risk of anti CCP-positive rheumatoid arthritis. The risk allele is (G); the odds ratio reported is 1.32 (95% confidence interval, 1.23 to 1.42; P=4x10-14) . rs3761847(G;G) associated with an increased risk of death (hazard ratio 3.96 [95% confidence interval 1.24-12.6], P = 0.020) as compared with (A;A) homozygote status. The excess mortality was attributed to deaths due to malignancies and sepsis but not cardiovascular disease (CVD). [PharmGKB:Non-Curated GWAS Results: TRAF1-C5 as a risk locus for rheumatoid arthritis--a genomewide study (Initial Sample Size: 1,493 cases, 1,831 controls; Replication Sample Size: 1,053 cases, 1,858 controls; Risk Allele: rs3761847-G...
0.63x decreased age-related macular degeneration risk
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news rs2511989 not associated with AMD rs2511989(A;A) had a protective effect against age related macular degeneration. Comparison of the rs2511989(A;G) genotype and the wild type (G;G) genotype yielded an odds ratio of 0.63 (CI: 0.47 to 0.84) for age-related macular degeneration. Comparison of rs2511989(A;A) homozygotes with (G;G) homozygotes resulted in an odds ratio of 0.44 (CI: 0.31 to 0.64). [PharmGKB:Curated A case-control study in a UK sample of 479 patients with age-related macular degeneration and 479 controls identified a highly significant association of this variant in intron six of the SERPING1 gene with age-related macular degeneration.]
+16% bilirubin levels increased risk of gallstones
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Xenobiotic metabolizing gene variants, dietary heterocyclic amine intake, and risk of prostate cancer. Serum bilirubin levels on ICU admission are associated with ARDS development and mortality in sepsis. [OMIM:UDP-GLYCOSYLTRANSFERASE 1 FAMILY, POLYPEPTIDE A1; UGT1A1] [GWAS:Serum bilirubin levels]
1.2x risk of coronary artery disease
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rs599839 and rs4970834 explain about 1% of the variation in circulating LDL-cholesterol levels. 'When we look at this particular genetic variance, of all the cholesterol variation among the population, 1% of it can be attributed to this particular locus,' said Sandhu. 'This is equivalent to more established genes for LDL regulation, particularly APOE.' rs646776 also linked. Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins found each minor allele to increase statin effectiveness by 1.3% (rs646776, β=−0.013, s.e.=0.002, P=1.05 × 10−9 and rs12740374, β=−0.013, s.e.=0.002, P=1.05 × 10−9). 23andMe blog coronary artery disease and heart attack SNP Risk Version Effect *rs646776 T 1.19 *rs1746...
Carrier of one CYP1A2*1F allele; Slow Caffeine Metabolizer. One copy of the slow caffeine metaboliser SNP, and one copy of the fast version. This makes you more strongly affected by drinking coffee, as caffeine is broken down slower in the liver. Supposedly this increases the risk of heart attacks, although other studies show caffeine is generally good for the heart. It also makes caffeine more effective at preventing Breast Cancer, Alzheimer's Disease, and Parkinson's disease. Too much caffeine will shrink your breasts.
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rs762551, also known as -164A>C or -163C>A, is a SNP encoding the CYP1A2*1F allele of the CYP1A2 gene. For historic reasons, the rs762551(C) allele is considered the wild-type, even though it is the rarer allele in most populations. The rs762551(A) allele is the 'fast metabolizer' allele known as CYP1A2*1F; the (C) allele is by comparison a slower metabolizer of certain substrates (including caffeine). In terms of genotypes, only rs762551(A;A) individuals are considered fast metabolizers. Individuals who are rs762551(A;C) heterozygotes or rs762551(C;C) homozygotes are both considered slow metabolizers. The CYP1A2 gene encodes a member of the cytochrome p450 family of proteins, which metabolize nutrients and drugs. One well known substrate of CYP1A2 is caffeine; individuals who are ca...
No reduction in heart disease risk from drinking alcohol This is the genotype known as B1B2, and as reported in the Mehlig et al. 2014 article, from a risk for coronary heart disease perspective this genotype is the same as the B1B1 genotype in showing no decrease in risk from consuming alcohol.
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rs708272, also known as the TaqIB polymorphism of the CETP gene, may influence the levels of the 'good' cholesterols, the high density lipoprotein (HDL) cholesterols. Generally, the B2 allele is considered to lead to higher HDL levels. However, high HDL cholesterol, at least when combined with another HDL raising SNP (rs1800588), doesn't appear to actually protect individuals from coronary artery disease, at least based on one study of ~800 Caucasian male patients. A similarly confusing picture emerges from a study of two populations of 10,000+ individuals each. The distribution of the CETP genotype was observed to be different in population-based studies compared with studies in populations selected by high cardiovascular risk, and contradictory results were seen when trying to figure out...
0.71x decreased risk for dry age related macular degeneration
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rs3775291 is a SNP in the TLR3 gene associated with an amino acid change in the corresponding protein. In the orientation as shown in dbSNP, the more common rs3775291(G) allele encodes a leucine while the rarer rs3775291(A) allele encodes a phenylalanine. rs3775291 has been associated with one form of age related macular degeneration (ARMD), specifically, the form known as 'dry' ARMD, also known as geographic atrophy. A study of 3 case-control groups of Americans of European descent, comprising about 900 ARMD patients in total, indicated that having one rs3775291(A) allele reduces the odds of having dry ARMD about 30%, and being a rs3775291(A;A) homozygote cuts your odds by more than half. Specifically, the odds ratio of having dry ARMD with one minor allele is 0.712 (CI: 0.50-1.0), and fo...
1.20x risk for breast cancer
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Based on a study of ~2500 female patients of European ancestry with sporadic postmenopausal breast cancer, this SNP in the FGFR2 showed the greatest risk. The risk allele is rs1219648(G), with a pooled odds ratio of 1.64 (CI:1.42-1.90) for rs1219648(G;G) homozygotes, and an odds ratio of 1.20 (CI: 1.07-1.42) for rs1219648(A;G) heterozygotes, compared with rs1219648(A;A) homozygotes. rs1219648 represents the SNP in the FGFR2 gene with the strongest association with breast cancer. However, nearby SNPs are almost as predictive. In particular, the following SNP alleles all have linkage values of 0.96 or greater with the rs1219648(G) allele in European populations: *rs2981579(A) *rs2420946(T) *rs11200014(A) An experimental rationale is presented indicating that this SNP is part of a haplotype t...
common/normal; aspirin use reduces colorectal cancer risk a bit
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rs2965667 is a SNP on chromosome 12p12.3 near the MGST1 gene. In a long-term study of ~17,000 individuals and aspirin or NSAID use, the few (4%) with either an (A;T) or (A;A) genotype were almost twice as likely to be diagnosed with colorectal cancer compared with (T;T) individuals among those taking anti-inflammatory drugs (prevalence, 28% vs 38%; (T;T) odds ratio 0.66 when taking aspirin/NSAID, CI: 0.61-0.70, p = 7.7 × 10e−33); prevalence, 35% vs 29%; (A;T) and (A;A) odds ratio 1.89 when taking aspirin/NSAID, CI: 1.27-2.81, p = .002). If this data is robust and all other factors are equal, this indicates that most people will lower their colorectal cancer risk by taking aspirin or NSAIDs, since most people have rs2965667(T;T) genotypes. However, the few people who are rs2965667(A;T) or a...
Normal risk of sexual dysfunction when taking SSRI Antidepressants.
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rs6311 (-1438A>G / A-1438G or -1438G>A / G-1438A) is a SNP located upstream (and within the promoter region of) HTR2A. Multiple Regulatory Variants Modulate Expression of 5-Hydroxytryptamine 2A Receptors in Human Cortex. The minor A allele of rs6311 reduces expression of a previously unannotated extension of the 5' untranslated region of HTR2A mRNA. rs6311 together with rs6314 have a modest effect on depression severity, when examined in the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study. Three (rs643627-rs594242-rs6311: A-C-T), two (rs594242-rs6311: C-T) and a single functional (rs6311: T) marker were protective against suicidal behavior. The complementary markers (rs594242-rs6311: G-C and rs6311: C) were associated with increased risk for non-violent and impu...
1.6x+ risk of ARMD
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rs2230199, a SNP in the complement component C3 gene, has been reported by several investigators to be associated with ARMD. The common allele at this SNP is known as Arg102; the variant and risk allele is known as Gly102. The risk allele, in orientation to the dbSNP entry for this rs#, is (G). In one of the largest case-control studies, the odds ratio associated with heterozygotes is 1.61, and for homozygotes, 3.26 (p = 4.5 x 10e-12). NEJM reports significant associate with ARMD. blog post [PharmGKB:Curated rs2230199 was found to be associated with risk of age-related macular degeneration in English and Scottish case-control studies.] [OMIM:MACULAR DEGENERATION, AGE-RELATED, 9; ARMD9] [GWAS:Age-related macular degeneration]
Slightly lower odds of developing CHD.
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[PharmGKB:Non-Curated Phenotype: In a GWAS, this SNP was significantly associated with plasma concentrations of LDL-C and apolipoprotein B. Study size: 6382. Study population/ethnicity: Caucasian women. Significance metric(s): LDL-C: p = 5.2 x 10 (-15);ApoB: p = 7.0 x 10(-18). Type of association: CO; GN] [OMIM:?] [GWAS:LDL cholesterol]
2x higher risk for skin cancer; possibly other cancers
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rs25487 is a SNP also known as Gln399Arg, located in the DNA repair gene XRCC1. The (A) allele encodes the Gln amino acid. In one study of ~1000 Caucasians, the rs25487(A;A) genotype had significantly reduced risk of both basal cell [BCC; odds ratio 0.7, CI: 0.4-1.0] and squamous cell cancer (SCC; odds ratio 0.6, CI: 0.3-0.9). In a study of ~300 Koreans, rs25487(A;G) and (G;G) genotypes had an approximately 2-fold increased risk of basal cell cancer compared to rs25487(A;A) individuals (adjusted odds ratio 2.324, CI: 1.11-4.86, respectively). A small study (113 cases) of Hispanics with non-small cell lung cancer found an odds ratio of 1.52 per rs25487(A) allele (CI: 1.01-2.28). A study of 200 patients with Hodgkin disease compared to controls concluded that some risk was associated with th...
1.2x increased risk for type-2 diabetes
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rs4402960 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.23 (CI: 1.11-1.36, p = 8.1 x 10e-5) associated with type-2 diabetes significantly associated with type-2 diabetes p = 0.00009; in 1,630 Japanese subjects and in 1,064 controls 1,638 type-2 diabetes patients and 1,858 controls *rs4402960 borderline (OR 1.10, 95% CI: 0.99-1.22). Neither rs4402960 or rs1470579 were found to be associated with type-2 diabetes in a study of 3,000 French Caucasians. This SNP was confirmed to be associated with type-2 diabetes in a study of 500+ Japanese patients plus pooled meta-analysis with 6 previous association studies (also of Japanese). Note: rs4402960 is fairly tightly linked (r<sup>2</sup>=0.87) with another IGF2BP2 gene SNP also asso...
increased risk of hypertension
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rs699 is a SNP in the angiotensin AGT gene that encodes a functional change. In most published literature, the name for this SNP is M235T, or perhaps Met235Thr, however its amino acid 268 (not 235) that varies based on the numbering in todays databases. rs699 is also occasionally known as C4072T. In any case, the rs699(C) allele encodes the threonine variant, which is associated with higher plasma angiotensin levels, and ultimately higher blood pressure leading to increased risk for hypertension associated disorders. This association was first reported in 1992 , and many studies, though not all, have replicated these findings. rs699 is also (generally) reported to be in tight linkage with rs5051, a neighboring SNP in the promoter of the AGT gene. rs699(C) has also been implicated as a risk...
Magnitude: 2
Frequency: 43.1%
References:13
Frequency: 43.1%
References:13
CYP2C19*17 ultra fast metabolizer; drug metabolism effects; also 0.77x decreased breast cancer risk
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rs12248560(T) defines the CYP2C19*17 allele, an ultra fast metabolizer phenotype of the CYP2C19 gene. CYP2C19*17 is likely to lead to less effective drug treatment by, for example, proton pump inhibitors (such as omeprazole) and antidepressants. On the other hand, cancer patients who are CYP2C19*17 carriers are more likely to benefit from tamoxifen treatment, presumably because they break it down more rapidly into the antiestrogenic metabolites endoxifen and 4-hydroxytamoxifen. A study of 1,000+ breast cancer patients showed a 0.77x decreased risk of breast cancer for carriers of a CYP2C19*17 allele (CI: 0.65-0.93, p = 0.005). Analysis of a subgroup of such carriers who were using hormone therapy for ten years or longer showed an even stronger effect (odds ratio 0.57, CI: 0.39-0.83, p = 0....
1.4x increased risk of Atrial Fibrillation and ischemic stroke. One defective copy. This affects the formation of the heart and gives a higher risk of Atrial Fibrillation (quivering of the top part of the heart), and Cardioembolic and Ischemic strokes (blocked blood flow to the brain). Based on several quality studies, and confirmed for Europeans and Asians. It's recommended to eat a heart-healthy diet, and only drink alcohol in moderation, to lower the risk.
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Two SNPs from chromosome 4q25, rs2200733 and rs10033464, were found to be associated with atrial fibrillation in a study of both European and Asian populations. The odds ratio associated with one or more copies of either risk allele was ~1.4x. The results derived from a study of 78 Italians with atrial fibrillation (AF) and atrial flutter (AFL) agree with previously reported findings from the Icelandic study (), which also found that the rs2200733(T) was associated with AF/AFL disease. In 1,661 Icelandic ischemic stroke samples and two large European replication sets combined, rs2200733 was associated with cardioembolic stroke (CES) (odds ratio 1.54, p = 8.05 x 10e-9). rs2200733 even showed association to ischemic stroke that was not classified as cardioembolic stroke. rs2200733 and rs1003...
Higher levels of serum bilirubin, associated with lower risk for coronary artery disease
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rs887829 is a SNP in the UGT1A1 gene. The minor allele of this SNP has been reported to be associated with higher levels of serum bilirubin, which has an inverse correlation with coronary artery disease. . This study of 2,000+ patients reports a recessive protective effect against coronary artery disease for the minor allele, with an age-adjusted odds ratio of 0.24 (CI: 0.10-0.60, p=0.0014). [PharmGKB:Curated This variant is in the promoter region of UGT1A1 and associated with serum bilirubin levels and hyperbilirubinemia in a genome wide association scan from 4300 Sardinian individuals.] [GWAS:Bilirubin levels]
~0.80x reduced cancer risk
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rs763110, also known as -844C>T, is a SNP in the FAS ligand FASLG gene. A meta-analysis of 19 published studies, including 11,105 cancer cases and 11,372 controls, concluded that the rs763110(C;T) and (T;T) genotypes were associated with a significantly reduced (about 0.80x) cancer risk of all cancer types.
1.9x higher risk for Crohn's disease
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rs17221417 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.29 (CI 1.13-1.46), and for homozygotes, 1.92 (CI 1.58-2.34). Pharmacogenetics: data, concepts and tools to improve drug discovery and drug treatment. Individual disease risk and multimetric analysis of Crohn disease. Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes. [OMIM:NUCLEOTIDE-BINDING OLIGOMERIZATION DOMAIN PROTEIN 2; NOD2]
Lower risk of dementia and Alzheimer's disease. Higher good cholesterol. One copy of a longevity gene. This seems to raise HDL ('good') cholesterol, and reduce the risk of dementia and Alzheimer's disease. It may slightly increase longevity. It has been particularly studied in Ashkenazi Jews.
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This SNP rs5882 in the CETP gene referred to as ILE405VAL and RSAI405V has been related to ageing and exceptional long life. A study in Ashkenazi Jews showed that individuals homozygotic for the G allele have significantly longer lifespans. New research also indicates that G homozygotes have an average of 70% less risk of dementia and Alzheimer's disease. The study also found that heterozygotes have a lower risk of dementia and Alzheimer's disease but more study is needed to determine the risk reduction for heterozygotes. See Association of a Functional Polymorphism in the Cholesteryl Ester Transfer Protein (CETP) Gene With Memory Decline and Incidence of Dementia and CETP Variant Linked to Slower Cognitive Decline and Reduced Dementia Risk . [PharmGKB:Curated Risk or phenotype-associated...
Common variant. Slightly shorter lifespan. Chemotherapy is less effective. Accelerated lung decline in smokers. African Americans have 2.15x risk of dying from colo-rectal cancer.
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This SNP, a variant in the TP53 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the G allele encodes an arginine at position 72 of the protein (where there's normally a proline), and the SNP is commonly called the Arg72 variant, although P72R and Arg72Pro are also common in the literature. Minor allele homozygotes, i.e. rs1042522(C;C) genotypes, live on average 3 years longer than major allele (G;G) homozygotes, based on a study of 9,200+ Danish individuals. The increased longevity is speculated to be related to the i...
0.58x decreased risk for esophageal cancer
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rs6505162 is a SNP located in the pre-miRNA region of mir423. The major allele is rs6505162(C). A study of 346 Caucasians with esophageal cancer found that compared with the homozygous wild-type genotype of rs6505162, individuals with the heterozygous and homozygous variant genotype had a significantly reduced esophageal cancer risk with odds ratios of 0.58 (CI: 0.41-0.82) and 0.43 (CI: 0.27-0.68), respectively. After stratifying by gender, smoking, and age, the authors discovered that the protective effect was significant only for individuals under 64 years of age, regardless of sex or whether they smoked. Other unfavorable genotypes (ie SNPs) were also identified that were not as significant as rs6505162, and the overall risk of esophageal cancer increased with increasing numbers of unfa...
2.1x increased risk of Crohn's disease
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rs1050152, a SNP in the SLC22A4 gene known as L503F, has been associated with an autoimmune disease, in this case, Crohn's disease, odds ratio = 2.1 (CI = 1.31–3.39, p = 0.002), based on a study of 203 cases and 200 controls. The risk allele is rs1050152(T). A nearby SNP (rs2631367) in the promoter region of the SLC22A5 gene defines a haplotype along with rs3792876, with odds ratio reported as similar for either SNP or the haplotype. Referring to the TC risk haplotype, the population risk attributable to heterozygotes was 19%, and for homozygous haplotype carriers, 27%. [PharmGKB:Non-Curated Higher gabapentin exposure and lower renal clearance/tubular secretion in individuals carrying this variant] [OMIM:?]
0.33x decreased risk for myocardial infarction if younger than 50
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rs2243250 is a SNP in the IL4 gene that is also known as the -589C>T SNP. In 300 patients younger than 50 years the rs2243250(T) allele was associated with a reduced risk of myocardial infarction (odds ratio 0.57, CI: 0.34-0.95). This result was replicated in another study, where carriers of one or two -589T alleles also had a reduced risk (odds ratio 0.67, CI: 0.47-0.95), with a strong protective effect of the -598T allele in homozygous -589T (odds ratio 0.33, CI: 0.10-1.05).
1.3x increased risk for multiple sclerosis
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The (C) allele of rs6897932, located in the alternatively spliced exon 6 of IL7RA gene and encoding the amino acid threonine rather than isoleucine at amino acid position 244, is associated with a slight increase (18%) in risk of developing multiple sclerosis. [PMID 17660817; Nature Genetics 39, 1083 - 1091 (2007) SG Gregory et al.] Note that the (C) allele is the most common at this position in all known populations and influences the ratios of the alternative isoforms (membrane bound and soluble) of the gene. blog post giving perspective on the significance of this snp a significant risk factor for multiple sclerosis in four independent (overall P = 2.9 x 10(-7)) influences the amount of soluble and membrane-bound isoforms of the protein by putatively disrupting an exonic splicing silenc...
higher risk for endometrial cancer
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rs4633 is a variant at codon 62 of the COMT gene, however, it does not change the amino acid sequence of the COMT protein. In a study of 150 (Caucasian) cases of endometrial cancer, a significant increase in rs4633(T;T) genotype was observed in patients compared to controls (OR = 2.39, CI: 1.31-4.37, p = 0.004). Furthemore, the frequency of the C-G haplotype of rs4633-rs4680 was significantly higher in controls (p < 0.0001) than in patients. This correlated with lower expression levels of the COMT protein in carriers of these alleles. pubmed 1180576 Schizophrenia Susceptibility Genetic basis for individual variations in pain perception and the development of a chronic pain condition [PharmGKB:Curated On the basis of subjects' pain responsiveness, haplotypes involving rs6269 (A/G), rs46...
Magnitude: 1.9
Frequency: 82.3%
Repute:Good
References:13
Frequency: 82.3%
Repute:Good
References:13
0.92x decreased risk of Atrial Fibrillation and cardioembolic stroke. This is the normal version which makes the heart form properly and makes people slightly less likely to get Atrial Fibrillation (quivering of the top chambers of the heart caused by chaotic electrical signals) and less likely to have a cardioembolic stroke (blocked blood flow to the brain). But also check the other SNP nearby (rs2200733) which affects Atrial Fibrillation even more. 23andMe gave this a 4 star confidence rating as it has been heavily studied. It has been confirmed in Europeans.
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Two SNPs from chromosome 4q25, rs2200733 and rs10033464, were found to be associated with atrial fibrillation in a study of both European and Asian populations. The odds ratio associated with one or more copies of either risk allele was ~1.4x. In 1,661 Icelandic ischemic stroke samples and two large European replication sets combined, rs10033464 was associated with cardioembolic stroke (CES) (odds ratio 1.27, p = 6.1 x 10e-4). rs2200733 and rs10033464 are strongly associated with AF in four cohorts of European descent. Variation in the 4q25 chromosomal locus predicts atrial fibrillation after coronary artery bypass graft surgery. Chromosome 4q25 variants and atrial fibrillation recurrence after catheter ablation. Common variants in KCNN3 are associated with lone atrial fibrillation. Associ...
Among asthmatics, 1.5x more likely to show less response to inhaled glucocorticoids
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rs37973 is a SNP in the promoter region of the glucocorticoid induced transcript 1 GLCCI1 gene on chromosome 7. Based on 4 populations totaling 900+ asthma patients, the rs37973(G) allele was associated (p = 0.0007, pooled data) with lower amounts of improvement of lung function in response to inhaled glucocorticoids such as budesonide. The mean (±SE) increase in forced expiratory volume in 1 second (FEV1) in treated rs37973(G;G) patients was about one third of that seen in rs37973(A;A) patients (3.2±1.6% vs. 9.4±1.1%). Based on dividing the response into highest vs lowest quartiles of response, the allelic odds ratio of falling into the lowest responding quartile based on an additive genetic model was calculated to be 1.52 (CI: 1.13 - 2.03). Genotype accounted for about 7% ...
1.6x higher overall CYP3A activity
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rs1057868, also known as A503V, is a relatively common variant defining the POR*28 allele of the P450 (cytochrome) oxidoreductase POR gene. The POR gene encodes a protein involved in electron transport of cytochrome p450 enzymes such as CYP3A4, CYP3A5 and CYP3A7. A study of 251 individuals from two independent studies (182 patients treated with methadone and 69 patients with clozapine) for CYP3A activity found that CYP3A SNPs themselves did not predict particularly well inter-individual variability in overall CYP3A activity. However, rs1057868(T;T) individuals had a 1.6x increased CYP3A activity compared to rs1057868(C) carriers (n=182, p=0.004), and the finding was replicated in a second independent dataset. The authors conclude that this POR gene SNP is a better predictor of overall CYP3...
Normal (higher) risk of Bipolar Disorder. This is the most common version of this SNP, so most people have this. But it is suspected of having a higher risk of Bipolar Disorder compared to the other rare versions of this SNP.
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Bipolar disorder failed to replicate in [PharmGKB:Non-Curated GWAS Results: A genome-wide association study implicates diacylglycerol kinase eta (DGKH) and several other genes in the etiology of bipolar disorder (Initial Sample Size: 461 cases, 563 controls; Replication Sample Size: 772 cases, 876 controls; Risk Allele: rs1012053-A).] [GWAS:Bipolar disorder]
1.12x increased risk for cutaneous melanoma
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rs13181 is a SNP of the XPD/ERCC2 gene. A meta-analysis of 20 studies, comprising 2,308 cases, ultimately concluded that the rs13181(G) allele is associated with increased cutaneous melanoma risk (odds ratio 1.12, CI: 1.03-1.21, p = 0.01; population attributable risk = 9.6%). Polymorphisms in XPD and TP53 and mutation in human lung cancer. Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method. ERCC1 and ERCC2 polymorphisms and adult glioma. [Correlation of genetic polymorphisms in nucleotide excision repair system to sensitivity of advanced non-small cell lung cancer patients to platinum-based chemotherapy]. Bladder cancer predisposition: a multigenic approach to DNA-repair and cell-cycle-control genes. Risk of non-Hodgk...
increased risk for auto-immune diseases
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The rs3087243 SNP is also known in the literature as the CT60 G>A or the +6230G>A polymorphism, and it is located in the CTLA4 gene. In Asian (Japanese) populations, the presence of an rs3087243(G) allele represents a 1.3 fold increased risk of autoimmune thyroid disease, and for those with autoimmune thyroid disease, a 1.5 fold increased risk of type-1 diabetes. However, in individuals without autoimmune thyroid disease, no association was seen between this SNP and type-1 diabetes. The authors speculate that earlier studies may have reported associations between this SNP and type-1 diabetes that were actually primarily based on the association with autoimmune thyroid disease. This same SNP, rs3087243, has also been implicated as a (minor) risk factor for developing rheumatoid arthri...
Minorly increased risk of mental illness and osteoarthritis
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rs16944 is a SNP in the interleukin 1, beta gene, a member of the cytokine family involved in the inflammatory response. The rs16944 G;G genotype is associated with risk for multiple mental illnesses. An increased risk for schizophrenia was found in a genetic association study of 2111 Caucasian individuals with an odds ratio of 1.24 (95% CI 1.09, 1.41) . Studies examining the brains of schizophrenic and bipolar individuals found reduced gray matter and hypoactivity associated with the G;G genotype. Additionally, this genotype is associated with impaired ability to achieve remission in a study of 256 Caucasian individuals with depression (odds ratio = 1.74; 95% confidence interval 1.2-4.3). The rs16944 A allele increases susceptibility to Osteoarthritis, with 1.80 times for heterozygotes (A...
in childhood acute lymphoblastic leukemia patients, worse response to vincristine (T;T) pediatric ALL patients being treated with vincristine have twice the risk of developing peripheral neuropathies compared to (C;C) and (C;T) patients, based on a preliminary study of ~300 patients.
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In a study of ~300 patients with childhood acute lymphoblastic leukemia (ALL) treated with vincristine, rs924607(T;T) patients, 28 of 50 (56%) developed at least 1 episode of grade 2 to 4 peripheral neuropathy. This was a significantly higher rate than in patients with (C;C) or (C;T) genotypes (58/271 patients; p = 2.4×10e-6). The severity of neuropathy was also greater in (T;T) patients.
Carrier of at least one CYP2D6 variants (non-CYP2D6*1)
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rs1135840, also known as 4180G>C or S486T, is a SNP in the CYP2D6 gene. The wild type (normal) allele at this SNP is (G). The (C) variant indicates the presence of a non-wild type CYP2D6 variant, but it appears in many different variants so it can not be used to determine the presence of any particular variant. Please be careful when interpreting results for this SNP as it is in dbSNP and SNPedia in minus orientation where the risk allele is C, but test results are usually in plus orientation where the risk allele is G. This SNP has an ambiguous flip which can make this very confusing. Polymorphisms affecting gene transcription and mRNA processing in pharmacogenetic candidate genes: detection through allelic expression imbalance in human target tissues. [PharmGKB:Curated Risk or phenot...
1.3x increased risk that pediatric inhaler use may make asthma worse
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rs1042713, also known as Arg16, G16R, and 16Arg>Gly, is a SNP in the adrenergic, beta-2-, surface receptor ADRB2 gene. The rs1042713(G) allele encodes the G/glycine form that is the more common one in most populations, while rs1042713(A) encodes the R/arginine residue at this position of the ADRB2 protein. A study of 1,182 young Scottish asthma patients (age, 3-22 years) concluded that rs1042713(A) alleles are significantly associated with 'exacerbations' of their condition, regardless of treatment regimens (odds ratio 1.30, CI: 1.09-1.55, p=0.003). This didn't hold true for patients using inhalers less than once per day; and it was particularly true for those receiving daily inhaled long- or short-acting beta(2)-agonist treatment (OR, 1.64, CI: 1.22-2.20, p=.001). This may therefore in...
Associated with (slightly) increased coffee consumption
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rs6968865 is a SNP located near the aryl hydrocarbon receptor AHR gene on ch 7p21. A meta-analysis of four GWAS studies of coffee consumption among a total of ~8,000 coffee drinkers of European ancestry found that the rs6968865(T) was strongly associated with increased consumption (p = 2.3 x 10e-11). The estimated effect was an increase of 0.2 cups a day per allele for both this SNP and one other (rs2472297).
1.2x increased risk for ALS
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rs2814707 is one of 2 SNPs from the ch 9p21.2 region associated in a large GWAS study with ALS risk, the other SNP being rs3849942. In this study, the reported odds ratio for rs2814707(A) was 1.22 (CI: 1.15 - 1.30, p = 4.72 x 10e-10). The odds ratio for the minor rs2814707(A) allele was 1.16 (p=7.45x10e-9). 23andMe blog rs2814707(T) 1.16x odds of ALS rs12608932(C) 1.2x odds of ALS [PharmGKB:Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.000002; OR: 5.2 (1.8, 16.7)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.] [OMIM:?]
possibly lower HDL cholesterol in women One report indicates that women (but not men) with this genotype may have slightly lower levels of HDL cholesterol, but other reports have not observed this.
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rs5370, also known as Lys198Asn or K198N, is a SNP in the endothelin-1 EDN1 gene on chromosome 6. The generally more common rs5370(G) allele encodes the Lys (K), and the rarer rs5370(T) allele encodes the Asn (N). Among the French-Canadian founder population of the Saguenay Lac St-Jean region of Quebec, rs5370(T) was associated with lower HDL cholesterol values in women (p = 1.3 x 10e-5), but not in men. In a study of 1,000+ Western Australians, no association was seen between HDL levels and rs5370. A study of ~400 rheumatoid arthritis patients found a 3x increase in the adjusted odds of being hypertensive for rs5370(T;T) homozygotes compared to (G;G) homozygotes (odds ratio 2.89, CI: 1.02 - 8.19, p=0.011). After adjustment for multiple potential confounders, haplotype analysis revealed an...
normal oral/throat cancer risk; more frequent alcohol consumption
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A SNP in rs1229984 encodes a form of the alcohol dehydrogenase ADH1B gene that significantly reduces the clearance rate of alcohol from the liver. This SNP is also known as Arg48His, with the (G) allele corresponding to the Arg and the (A) to the His. Known in the literature as ADH2*2 or sometimes ADH1B*2, the allele with increased activity (meaning more rapid oxidation of ethanol to acetaldehyde) is His48, encoded by rs1229984(A). Individuals with one or especially two ADH2*2 alleles, ie genotypes rs1229984(A;G) or rs1229984(A;A) are more likely to find drinking unpleasant and have a somewhat reduced risk for alcoholism. A study of over 3,800 cases of 'upper aerodigestive' cancers (mouth/throat, voice box, and esophageal cancers) concluded that the rs1229984(A) allele (in dbSNP orientatio...
1.1x increased risk for schizophrenia
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rs1344706 is a SNP in the ZNF804A gene, and it is probably the first SNP to have been reported as achieving genome-wide significance for psychosis. Reviews the literature, and concludes that rs1344706 is 'robustly, if modestly' associated with increased risk for schizophrenia. A genome-wide association study of schizophrenia (479 cases, 2,937 controls) followed by additional testing and a meta-analysis concluded that the strongest evidence for association was around ZNF804A (rs1344706; p = 1.61 x 10e-7) and that the finding was strengthened when the affected phenotype included bipolar disorder (p = 9.96 x 10e-9). Executive function, neural circuitry, and genetic mechanisms in schizophrenia. Apoptotic engulfment pathway and schizophrenia. Persistence criteria for susceptibility genes for sc...
References:1
Frequency: 43.1%
References:1
References:1
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rs2297404, rs2230808, and rs2020927 haplotype (CAC) was more prevalent in the Alzheimer's disease group (0.323 in AD vs. 0.202 in control); while haplotype1 (TGG) was over-represented in the healthy controls (0.595 in control vs. 0.493 in AD) ABCA1 modulates CSF cholesterol levels and influences the age at onset of Alzheimer's disease. ABCA1 polymorphisms and Alzheimer's disease. Apolipoprotein E levels in cerebrospinal fluid and the effects of ABCA1 polymorphisms. The effect of ABCA1 gene polymorphisms on ischaemic stroke risk and relationship with lipid profile. Genetic-epidemiological evidence on genes associated with HDL cholesterol levels: a systematic in-depth review. A survey of ABCA1 sequence variation confirms association with dementia. A polymorphism of the ABCA1 gene confers sus...
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rs2230806, also known as Arg219Lys or R219K, is a SNP in the ABCA1 ATP-binding cassette, sub-family A (ABC1), member 1 gene. The rs2230806(G) allele encodes the arginine (R), and the (A) allele encodes the lysine (K). A meta-analysis published in 2011 comprising 22 studies with 6597 cases and 15,369 controls studied the association between the rs2230806 and risk for coronary artery disease. Overall, rs2230806(A) significantly associated with a higher HDL-C level in Asians and does lower the risk (odds ratio 0.76, CI: 0.68-0.85, p=3.78e-07) of coronary artery disease in Asians and Caucasians. ABCA1 modulates CSF cholesterol levels and influences the age at onset of Alzheimer's disease. Gender-specific association of ATP-binding cassette transporter 1 (ABCA1) polymorphisms with the risk of l...
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Genetic variants and prostate cancer risk: candidate replication and exploration of viral restriction genes.
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Altered brain-derived neurotrophic factor blood levels and gene variability are associated with anorexia and bulimia. Brain-derived neurotrophic factor ( BDNF) gene: no major impact on antidepressant treatment response. Association analysis of brain-derived neurotrophic factor gene polymorphisms in asthmatic families. Pharmacogenetics of antidepressant response. Brain-derived neurotrophic factor (BDNF) gene: a gender-specific role in cognitive function during normal cognitive aging of the MEMO-Study? Brain-derived neurotrophic factor gene polymorphisms, neurotransmitter levels, and depressive symptoms in an elderly population.
References:8
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Brain-derived neurotrophic factor does not influence age at neurologic onset of Huntington's disease. The influence of serotonin- and other genes on impulsive behavioral aggression and cognitive impulsivity in children with attention-deficit/hyperactivity disorder (ADHD): Findings from a family-based association test (FBAT) analysis. Evidence of association between brain-derived neurotrophic factor gene and bipolar disorder. Brain-derived neurotrophic factor ( BDNF) gene: no major impact on antidepressant treatment response. Molecular differentiation of schizoaffective disorder from schizophrenia using BDNF haplotypes. The role of BDNF genetic polymorphisms in bipolar disorder with psychiatric comorbidities. Pharmacogenetics of antidepressant response. Linkage and association study of neur...
References:5
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[PharmGKB:Curated This variant in the 5' untranslated region of BDNF was associated with antidepressant response after adjusting for age, sex, medication, and baseline score on the 21-item Hamilton Depression Rating Scale in a study of 264 controls and 272 Mexican Americans with major depressive disorder.]
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several articles in pubmed but still lacks any clear effects.
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Significant association of BDNF haplotypes in European-American male smokers but not in European-American female or African-American smokers. Cholinergic nicotinic receptor genes implicated in a nicotine dependence association study targeting 348 candidate genes with 3713 SNPs. Brain-derived neurotrophic factor and risk of schizophrenia: an association study and meta-analysis. A generalized combinatorial approach for detecting gene-by-gene and gene-by-environment interactions with application to nicotine dependence. BDNF variability in opioid addicts and response to methadone treatment: preliminary findings. Gene-gene interactions among CHRNA4, CHRNB2, BDNF, and NTRK2 in nicotine dependence. Evidence of association between brain-derived neurotrophic factor gene and bipolar disorder. Associ...
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[GWAS:None]
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[PharmGKB:Curated This SNP at chromosome 9 is significantly associated with HNRPD expression (located on chromosome 4), and daunorubicin IC50 in CEU population using International HapMap cell lines.]
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Overlap of disease susceptibility loci for rheumatoid arthritis and juvenile idiopathic arthritis. Genetic variants in the prediction of rheumatoid arthritis. Investigation of rheumatoid arthritis susceptibility genes identifies association of AFF3 and CD226 variants with response to anti-tumour necrosis factor treatment. [PharmGKB:Curated This SNP located on chromosomes 10p15 is associated with susceptibility to rheumatoid arthritis in a validation study of 4,106 individuals with rheumatoid arthritis and an expanded reference group of 11,238 subjects.] [GWAS:Rheumatoid arthritis]
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[GWAS:Acute lymphoblastic leukemia (B-cell precursor)]
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23andMe blog blood pressure [GWAS:Diastolic Blood Pressure]
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Genetic variation in the choline acetyltransferase (CHAT) gene may be associated with the risk of Alzheimer's disease. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. ApoE-epsilon 4-dependent association of the choline acetyltransferase gene polymorphisms (2384G>A and 1882G>A) with Alzheimer's disease. Choline acetyltransferase variants and their influence in schizophrenia and olanzapine response. Combining fMRI and SNP data to investigate connections between brain function and genetics using parallel ICA. Regional association-based fine-mapping for sodium-lithium countertransport on chromosome 10. Identification of pharmacogenetic markers in smoking cessation therapy. Replication and extension of association of choline a...
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Candidate gene association studies of genes involved in neuronal cholinergic transmission in Alzheimer's disease suggests choline acetyltransferase as a candidate deserving further study. Genetic variation in the choline acetyltransferase (CHAT) gene may be associated with the risk of Alzheimer's disease. ApoE-epsilon 4-dependent association of the choline acetyltransferase gene polymorphisms (2384G>A and 1882G>A) with Alzheimer's disease. Choline acetyltransferase variants and their influence in schizophrenia and olanzapine response. Combining fMRI and SNP data to investigate connections between brain function and genetics using parallel ICA. Replication and extension of association of choline acetyltransferase with nicotine dependence in European and African American smokers.
normal
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A case-control study of 471 Italian late-onset Alzheimer's disease patients aged 60 years or older, and 254 subjects with no neurodegenerative disorders serving as the control group, found that the rs2177369(G;G) genotype (in dbSNP orientation) a risk factor with an odds ratio of 1.56 (CI: 1.10-2.22, p = 0.01). Refreshingly, the authors call their results 'far from definitive'.
Frequency: 54.0%
References:5
References:5
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Replication analysis confirms the association of ARID5B with childhood B-cell acute lymphoblastic leukemia. [PharmGKB:Curated This SNP located in intron 3 of the ARID5B gene differed between pediatric acute lymphoblastic leukemia (ALL) and non-ALL groups (rs10994982, P = 5.7 x 10(-9), OR = 1.62) and also distinguished B-hyperdiploid ALL from other subtypes (rs10994982, P = 0.003, OR 1.72). This SNP was in linkage disequilibrium with rs10821936 (r2 = 0.42, P < 1 10-10). The study found found that the same alleles of this ARID5B SNP rs10994982 that were associated with B-hyperdiploid ALL were also associated with greater methotrexate polyglutamate accumulation (P = 0.021).] [OMIM:?]
Frequency: 47.8%
References:12
References:12
normal
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[PharmGKB:Curated Phenotype: This SNP is associated with risk of childhood acute lymphoblastic leukemia in blacks and also with racial differences in frequency of the disease . The frequency of the risk allele, C, was significantly higher(0.33) in black children with ALL enrolled in St. Jude clinical trials than in controls of African ancestry (0.163 ASW,0.20 YRI). Risk Allelle: C allele. Study size/population/ethnicity: patients-93 black children with newly diagnosed ALL; controls- 112 unrelated subjects of African ancestry from the HapMap project(52 from American Southwest and 60 from Yoruba) . Significance metric(s): OR = 2.08; 95% CI = 1.32-3.27; p = 0.0015 . Type of association: CO; GN. The association of the C allele (one or two copies) with risk for the ALL subtype B-hyperdiploid AL...
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[GWAS:Systemic lupus erythematosus]
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[PharmGKB:Curated Risk or phenotype-associated allele: C Phenotype: The CHST3:rs4148943 C variant was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0001 Type of association: PD; CO]
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[PharmGKB:Curated Risk or phenotype-associated allele: C Phenotype: The CHST3:rs4148945 C variant was associated with positive clincial response (partial or complete response) to treatment and toxicity to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.011 (response); p = 0.010 (TOX) Type of association: PD; CO; TOX]
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[PharmGKB:Curated Risk or phenotype-associated allele: C Phenotype: The CHST3:rs4148947 C variant was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0023 Type of association: PD; CO]
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[PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: The CHST3:rs4148950 A variant was associated with positive clincial response (partial or complete response) to treatment and toxicity to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s):p = 0.024 (response); p = 0.006 (TOX) Type of association: PD; CO; TOX]
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[PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: The CHST3:rs1871450 A variant was associated with positive clincial response (partial or complete response) to treatment and toxicity to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.048 (response); p = 0.006 (TOX) Type of association: PD; CO; TOX]
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[PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: The CHST3:rs730720 A variant was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0034 Type of association: PD; CO]
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[PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: The CHST3:rs12418 A variant was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0005 Type of association: PD; CO]
References:1
0.62x reduced risk for sarcoidosis
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rs1049550, also known as R230C, is a SNP in the annexin A11 ANXA11 gene. 499 German individuals with sarcoidosis and 490 controls; Validation in an independent sample 1,649 cases, 1,832 controls. rs2789679: P = 3.0 x 10(-13), rs7091565: P = 1.0 x 10(-5)rs1049550, T > C, R230C was found to be strongly associated with sarcoidosis. rs2789679 P = 3.0 x 10(-13), rs7091565: P = 1.0 x 10(-5), allele-based test). Extensive fine mapping located the association signal to a region between exon 5 and exon 14 of ANXA11. A common nonsynonymous SNP (rs1049550, T > C, R230C) was found to be strongly associated with sarcoidosis Note that several ANXA11 SNPs are all tightly linked: rs1953600, rs2573346, rs2784773 and rs1049550. [PharmGKB:Curated A genome-wide association study in 499 German individua...
~10% more likely to respond to citalopram
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rs1954787, located in an intron of the GRIK4 gene, was found to be associated with a somewhat increased rate of successful response to treatment of depression with the drug citalopram. From the abstract of this article: 'The effect size of (this) GRIK4 marker alone was modest, but homozygote carriers of the treatment-response-associated marker alleles of both the GRIK4 and HTR2A (see rs7997012) genes were 23% less likely to experience nonresponse to (citalopram) treatment relative to participants who did not carry any of these marker alleles.' * See also Anxiety Blog posting [PharmGKB:Curated A study in 1,816 eligible patients from the STAR*D cohort found that genetic variation in a kainic acid-type glutamate receptor is reproducibly associated with response to the antidepressant citalopr...
Frequency: 32.7%
References:1
References:1
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[PharmGKB:Non-Curated ABCC2*2 (−1019a>G) is associated with lower irinotecan clearance and with significant reduction in severe diarrhea in cancer patients.]
1.6x risk for ICP
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rs3740066, a SNP in the ABCC2 gene, is reported to be associated with a higher risk of developing intrahepatic cholestasis of pregnancy (ICP) based on a study of ~70 Argentinian patients. ICP is associated with increased fetal risks such as premature birth or intrauterine death. The risk allele is rs3740066(A), and the odds ratio for homozygous rs3740066(A;A) mothers is 4.44 (CI: 1.83 - 10.78), and for heterozygous mothers 1.65 (CI: 0.76 - 3.64), compared to rs3740066(G;G) mothers. [PharmGKB:Curated The AUCs of irinotecan, SN-38, SN-38 glucuronide, and APC are influenced by rs3740066, rs2306283, rs35605, rs10276036, and rs717620 .]
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rs12762549 and rs11045585 can be used to predict whether docetaxel will induced leukopenia/neutropenia, according to a study of ~100 Japanese patients. When patients were classified into three groups by the scoring system based on the genotypes of these two SNPs, patients with a score of 1 or 2 were shown to have a significantly higher risk of docetaxel-induced leukopenia/neutropenia as compared to those with a score of 0 (P = 0.0000057; odds ratio [OR], 7.00; 95% CI [confidence interval], 2.95-16.59). This prediction system correctly classified 69.2% of severe leukopenia/neutropenia and 75.7% of non-leukopenia/neutropenia into the respective categories. [PharmGKB:Curated In a case control study using samples from BioBank Japan, the G allele of rs12762549 was associated with docetaxel-ind...
References:5
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rs1800544 (C-1291G) is a SNP located in the promoter region of ADRA2A (adrenergic receptor alpha 2A). GG genotype carriers had significantly higher consumption of sweet food products (Estonian Children Personality Behavior and Health Study subset, n = 419) GG genotype carriers had significantly higher scores on an assessment of depression, and significantly lower scores on morality and orderliness compared to CC carriers. girls with CC and CG genotypes scored higher than boys with the same genotypes on an assessment of extraversion. boys with GG genotypes, however, scored higher than girls with GG genotypes. GG genotype assoc. w/ higher scores of inattention Food Preference [OMIM:ALPHA-2A-ADRENERGIC RECEPTOR; ADRA2A]
depends on [[rs1801252]]
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Also known as Arg389, variation at this SNP, located in the ADRB1 gene, may encode either the amino acid glycine or arginine at amino acid position 389 of the corresponding protein, the beta-1 adrenergic receptor (hence why it is frequently called Arg389Gly). This protein is the target of beta blocker drugs, and so how well the drug works to help lower a patients high blood pressure depends in part on this SNP. The status of this SNP is often reported together with the status of SNP rs1801252, which encodes an amino acid variant at position 49 of the same (ADRB1) protein. The rs1801253(G) allele encodes the glycine. One of the best known studies of the effects of these 2 separate SNPs on the average efficacy of the beta blocker metoprolol in lowering blood pressure (BP) can be summarized f...
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[PharmGKB:Curated Minor allele G is associated with LQTS1(tagging SNP for QTL haplotype block).]
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nature type-2 diabetes *rs2237895, P = 7.3 times 10-9; OR = 1.32, 95% CI = 1.20–1.45 SNPs in KCNQ1 are associated with susceptibility to type 2 diabetes in East Asian and European populations. Meta-analysis in genome-wide association studies. Genetic variation in KCNQ1 associates with fasting glucose and beta-cell function: a study of 3,734 subjects comprising three ethnicities living in Singapore. Common variants in KCNQ1 are associated with type 2 diabetes and impaired fasting glucose in a Chinese Han population. Polymorphisms in KCNQ1 are associated with gestational diabetes in a Korean population. KCNQ1 gene polymorphisms are associated with lipid parameters in a Chinese Han population. Variants in KCNQ1 increase type II diabetes susceptibility in South Asians: a stu...
References:2
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[PharmGKB:Curated A haplotype of RRM1 (2455 A>G and 2464 G>A) was associated with a lower frequency of neutropenia in advanced breast cancer patients treated with gemcitabine.]
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[PharmGKB:Curated A haplotype of RRM1 (2455 A>G and 2464 G>A) was associated with a lower frequency of neutropenia in advanced breast cancer patients treated with gemcitabine.]
References:4
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[PharmGKB:Curated Risk or phenotype-associated allele: C. Phenotype: In a study of patients with major depressive disorder, individuals with the CC genotype had poorer response to paroxetine than those with the A variant. Study size: 111. Study population/ethnicity: Individuals with a major depressive disorder treated with paroxetine. Significance metric(s): OR = 0.075 (95% CI 0.019-0.295); p < 0.001. Type of association: PD.]
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A PAI-1 (SERPINE1) polymorphism predicts osteonecrosis in children with acute lymphoblastic leukemia: a report from the Children's Oncology Group. SNP combinations in chromosome-wide genes are associated with bone mineral density in Taiwanese women.
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The association between type-1 diabetes and rs5215 is mentioned as being replicated in ; there is also a 90% correlation between rs5215 and rs5219. [GWAS:Type 2 diabetes]
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commonly referred to as A779C Only for Hispanics, individuals who have a genoset composed of rs1799913(C;C) and rs7963720(T;T) are reported to be at 14x higher risk for developing heroin addiction (CI:0.83-244.63, p=0.012). Again, only for Hispanics, individuals having a genoset composed of rs1799913(C;C) and rs4290270(T;T) are reported to be at 9x higher risk for developing heroin addiction (CI:0.5-153, p=0.063). Association between 5-HT2A, TPH1 and GNB3 genotypes and response to typical neuroleptics: a serotonergic approach. Tryptophan hydroxylase gene 1 (TPH1) variants associated with cerebrospinal fluid 5-hydroxyindole acetic acid and homovanillic acid concentrations in healthy volunteers. [OMIM:TRYPTOPHAN HYDROXYLASE 1; TPH1]
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commonly referred to as A218C rs211105, rs1800532 and rs7933505 related to schizophrenia [OMIM:TRYPTOPHAN HYDROXYLASE 1; TPH1]
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Tryptophan hydroxylase 2 (TPH2) gene variants associated with ADHD. Preferential transmission of paternal alleles at risk genes in attention-deficit/hyperactivity disorder. The analysis of 51 genes in DSM-IV combined type attention deficit hyperactivity disorder: association signals in DRD4, DAT1 and 16 other genes.
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rs1386494 is a SNP in the tryptophan hydroxylase 2 (TPH2) gene on chromosome 12. It is located about 20,000 bp from the 5' end of the gene. This SNP has been found to be associated with various mental health disorders. TPH1 and TPH2 are two isoforms of the rate-limiting enzyme for the biosynthesis of 5-HT (serotonin), a neurotransmitter involved in many neurological processes. Both isoforms have been studied extensively as genetic markers of mental health. Many association studies have linked the TPH1 gene to suicidality, alcoholism and depression. However, the second TPH isoform was not discovered until more recently, when it was observed that TPH1 knockout mice were still able to produce normal levels of 5-HT. It has been shown to be expressed exclusively in the brain, suggesting that it...
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[PharmGKB:Curated Risk or phenotype-associated allele: GG genotype Phenotype: Using a Quantitative Transmission Disequilibrium Test (QTDT), this variant was significantly associated with increased gene expression of IL1B (P = 7 ? 10?7) and etoposide toxicity based upon IC50 values in cell lines from 30 parent-child trios. In combination, rs10018204, rs11222869, rs16965867, rs1846644, and rs6539870 were significant predictors of etoposide IC50, accounting for 55% of the etoposide IC50 variation in Caucasians. Study size: 87. Study population/ethnicity: 87 European descent Caucasians. Significance metric(s): p = 0.00002. Type of association: FA; GN.]
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Common variation in the SERPING1 gene is not associated with age-related macular degeneration in two independent groups of subjects. [PharmGKB:Curated This variant is associated with age-related macular degeneration.]
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[GWAS:Metabolite levels]
Frequency: 54.0%
References:1
References:1
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Polymorphisms in the galanin gene are associated with symptom-severity in female patients suffering from panic disorder.
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Synergistic association of mitochondrial uncoupling protein (UCP) genes with schizophrenia. A genetic association analysis of cognitive ability and cognitive ageing using 325 markers for 109 genes associated with oxidative stress or cognition. Ala55Val polymorphism on UCP2 gene predicts greater weight loss in morbidly obese patients undergoing gastric banding. Lack of association between uncoupling protein-2 Ala55Val polymorphism and incident diabetes in the atherosclerosis risk in communities study. Ser1369Ala variant in sulfonylurea receptor gene ABCC8 is associated with antidiabetic efficacy of gliclazide in Chinese type 2 diabetic patients. Human uncoupling protein 2 and 3 genes are associated with obesity in Japanese. Physiogenomic comparison of edema and BMI in patients receiving ros...
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Data-mining analysis suggests an epigenetic pathogenesis for type 2 diabetes. Genetic prediction of future type 2 diabetes. Interaction between the UCP2-866G/A, mtDNA 10398G/A and PGC1alpha p.Thr394Thr and p.Gly482Ser polymorphisms in type 2 diabetes susceptibility in North Indian population. Association between obesity and insulin resistance with UCP2-UCP3 gene variants in Spanish children and adolescents. Association of genetic variants with chronic kidney disease in Japanese individuals. Polymorphisms of the UCP2 gene are associated with proliferative diabetic retinopathy in patients with diabetes mellitus. Interaction between the UCP2 -866 G>A polymorphism, diabetes, and beta-blocker use among patients with acute coronary syndromes. Effect of the common -866G/A polymorphism of the u...
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Genetic variants in the UCP2-UCP3 gene cluster and risk of diabetes in the Women's Health Initiative Observational Study.
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[GWAS:None]
hypertension not a risk factor for sudden cardiac death
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rs187238, also known as -137 G/C, is a SNP in the interleukin 18 IL18 gene. Based on studying autopsies of 700 men in the Helsinki Sudden Death Study, there was a significant interaction between IL-18 genotype and hypertension impacting on the risk of sudden cardiac death (SCD) due to coronary heart disease (CHD). Among rs187238(G;G) homozygotes, hypertension was a major risk factor for SCD due to CHD (adjusted odds ratio 3.75, CI:1.78-7.91, p < 0.001) and hypertension also associated with larger coronary atherosclerotic plaque areas (p = 0.002) and the occurrence of complicated plaques (adjusted OR 8.38, CI: 2.39-29.33, p < 0.001). Among rs187238(C) allele carriers, hypertension was not a significant risk factor for CHD-related SCD or CAD and did not associate with the development o...
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rs1946518 and rs1946519 may influence cervical cancer
1.4x higher schizophrenia risk
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rs6277 (957C>T, Pro319Pro) is one of several SNPs in the dopamine receptor DRD2 gene. In a study of 300+ Russian patients with schizophrenia, the rs6277(C) allele was associated with higher risk. From a pooled meta-study (total of 4 other reports plus this one) the allelic odds ratio is 1.42 (CI: 1.26-1.61, p<0.00005), and the genotypic odds ratio for the (C;C) genotype was 1.6 (CI: 1.32-1.95, p<0.00005). Note that rs6275 and rs6277 are only 18bp apart, hence their very tight linkage (r<sup>2</sup>=1). gs278 reflects a gene-gene interaction between this SNP and a NR3A SNP, rs10989591, in which older adults with a particular combination of genotypes at these two (independent) loci are reported to exhibit better episodic memory. C allele associated significantly (p = 0.0...
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rs6275/DRD2 and rs4680/COMT useful in predicting disease risk among schizophrenia patients See also rs6277. [PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: The average and maximum daily methadone doses were significantly associated with the DRD2 rs6275C>T SNP (P=0.016 and 0.005 for average and maximum dose, respectively). Carriers of the variant rs6275T allele needed higher methadone doses than noncarriers. Study size: 85. Study population/ethnicity: Caucasian. Type of association: GN.]
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[PharmGKB:Curated Risk or phenotype-associated allele: C Phenotype: Patients homozygous for the rs4436578-C allele were at increased risk of body weight gain as compared with the heterozygotes and those of the rs4436578-TT genotype after atypical antipsychotics treatment Study size: 479 chronic inpatients with schizophrenia Study population/ethnicity: Chinese Significance metric(s): OR = 3.36 (95% confidence interval=1.62 approximately 7.00) Type of association: GN]
Frequency: 13.3%
References:1
References:1
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Genome bioinformatic analysis of nonsynonymous SNPs. Physiogenomic analysis of localized FMRI brain activity in schizophrenia. HTR3B is associated with alcoholism with antisocial behavior and alpha EEG power--an intermediate phenotype for alcoholism and co-morbid behaviors. Pharmacogenetics of antidepressant response. Are serotonin 3A and 3B receptor genes associated with suicidal behavior in schizophrenia subjects? [OMIM:5-@HYDROXYTRYPTAMINE RECEPTOR 3B; HTR3B]
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[PharmGKB:Curated This variant is found to be a risk marker for statin induced myalgia]
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Rs1062613 (C178T, Pro16Ser) is located within the 5' UTR of HTR3A and may effect HTR3A expression. reporter constructs containing the T allele showed increased HTR3A expression compared to the C allele CC and CT carriers associated with higher harm avoidance (p = 0.04) scores in 2 sample groups of Swedish women (366 in total), and non-conformity in 1 sample no significant association between treatment-resistant schizophrenia and Rs1062613, however, maintenance neuroleptic dose was significantly higher for TT carriers (p = 0.041) [PharmGKB:Curated This promoter variant regulates expression of the gene. The T allele is associated with increased expression.]
more likely to gain weight if taking olanzapine
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rs5092 is a SNP in the apolipoprotein A4 APOA4 gene. In a study of 67 mostly Caucasian patients prescribed the atypical antipsychotic olanzapine, carriers of a rs5092(G) allele were less likely to gain significant weight compared to rs5092(A;A) carriers, as assessed by physiogenomic analysis of corresponding weight profiles. Two other SNPs, rs4765623 and rs7412, were also significantly associated with weight profiles in these patients.
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[PharmGKB:Curated This promoter variant is associated with hyperlipidemia (elevated triglyceride levels) for HIV-infected individuals treated with ritonavir.] [OMIM:?]
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[PharmGKB:Curated This promoter variant is associated with hyperlipidemia (elevated triglyceride levels) for HIV-infected individuals treated with ritonavir.] [OMIM:?]
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rs5128 (C3238G/3238C>G) is a SNP within the 3' UTR of APOC3 (Apolipoprotein C3). subjects with GC/GG genotypes and diabetes exhibited sig. higher triglyceride (p=0.004), total cholesterol (p=0.003) and glucose (p=0.016) compared to CC subjects [PharmGKB:Curated This 3' UTR variant is associated with hyperlipidemia (elevated triglyceride levels) for HIV-infected individuals treated with ritonavir.]
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[PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: This SNP was associated with a greater reduction in total cholesterol after at least 1 week of statin use. This was not replicated in a second cohort. Study size: 546 (original cohort); 100 (replication cohort). Study population/ethnicity: People taking statins; age 55 or older; Rotterdam Study; Netherlands. Significance metric(s): p = 0.05 (original); p = 0.975 (replication) Type of association: PD.]
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[OMIM:MYOCARDIAL INFARCTION, DECREASED SUSCEPTIBILITY TO]
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Association between SLC6A12 gene and negative symptoms of schizophrenia in Korean population.
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[GWAS:Metabolite levels]
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23andMe blog rs1006737 or (rs2159100) Each T at this SNP increased the odds of bipolar disorder by 1.18 times compared to having two CC copies [PharmGKB:Curated A genome-wide association analysis study in 4,387 cases and 6,209 controls identified a strong association of this variant in the CACNA1C gene with bipolar disorder.] [OMIM:MAJOR AFFECTIVE DISORDER 9; MAFD9] [GWAS:Bipolar disorder]
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[PharmGKB:Curated In a case-control study (258 cases; 774 controls) performed in patients residing in the mainland U.S. or Puerto Rico and who had hypertension and stable coronary artery disease, this SNP was found to be related to primary outcome of atenolol vs. verapamil SR - based treatment. AA genotype was associated with 46% reduction in primary outcome for patients on verapamil SR-based treatment compared to atenolol-based treatment (odds ratio 0.54; 95% CI 0.32 to 0.92), AG genotype showed no difference in primary outcome between the two strategies (odds ratio 1.47; 95% CI 0.86 to 2.53), and GG subjects had more than 4 fold increased risk of primary outcome on verapamil SR-based treatment as opposed to atenolol-based treatment (odds ratio 4.59; 95% CI 1.67 to 12.67). Study size: 258...
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rs1800693 is a SNP in the tumor necrosis factor receptor superfamily, member 1A TNFRSF1A gene. A large study (~5,000 patients) found two SNPs in the TNFRSF1A gene that each (independently) increase risk for multiple sclerosis, rs1800693 and rs4149584. This SNP, rs1800693, is more common but increases risk less; the odds ratio is reported as 1.2 (CI: 1.10-1.31, p=1.6x10(-11)). [OMIM:?] [GWAS:Multiple sclerosis]
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Genetic polymorphisms of tumour necrosis factor receptor superfamily 1A and 1B affect responses to infliximab in Japanese patients with Crohn's disease. Comprehensive follow-up of the first genome-wide association study of multiple sclerosis identifies KIF21B and TMEM39A as susceptibility loci.
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Optimization of candidate-gene SNP-genotyping by flexible oligonucleotide microarrays; analyzing variations in immune regulator genes of hay-fever samples. Genetic polymorphisms of tumour necrosis factor receptor superfamily 1A and 1B affect responses to infliximab in Japanese patients with Crohn's disease. Genome-wide association scan identifies candidate polymorphisms associated with differential response to anti-TNF treatment in rheumatoid arthritis. Polymorphisms in apoptosis-related genes and survival of patients with early-stage non-small-cell lung cancer. Genetic variants in inflammation-related genes are associated with radiation-induced toxicity following treatment for non-small cell lung cancer.
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[GWAS:None]
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[PharmGKB:Curated Risk or phenotype-associated allele: SLCO1B3: T334. Phenotype: The metabolic ratio of glucuronidated mycophenolic acid (MPAG) to mycophenolic acid (MPA) showed a very significant decrease in carriers of the SLCO1B3 T334 allele (p = 0.0001). Carriers of at least one SLCO1B3 T334 allele (n = 22) had a 1.42-fold higher (p = 0.0003) MPA AUC(0-12 hours) and a 1.38-fold higher (p = 0.0010) Cmax as compared with carriers of the 334GG genotype (n = 48). Patients carrying 334 TT or TC genotypes (n = 22) had significantly higher MPA AUC(4-9 hours) than patients carrying the CC genotype (n = 48; p = 0.0027). However, they also had higher AUC(0-4 h) (p = 0.0008), resulting in an unchanged AUC(4-9 h)/AUC(0-9 h) ratio (p = 0.4945). In the subgroups of patients cotreated with sirolimus ...
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[PharmGKB:Curated Risk or phenotype-associated allele: SCLO1B3 haplotype formed by 112Ser>Ala (rs4149117, 334T>G) and 223Met>Ile (rs7311358, 699G>A). Phenotype: HEK293 cells transiently expressing the SCLO1B3 334G-699A haplotype or reference haplotype were incubated in the presence of increasing concentrations of mycophenolic acid phenyl-glucuronide (MPAG) for 10 min. The uptake of MPAG according to the SCLO1B3 334G-699A haplotype was markedly lower than in cells expressing the reference sequence 334T-669G. Type of association: GN; FA; PK]
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rs2306283 (Asn130Asp/N130D, A388G/388A>G) is a SNP within SLCO1B1 (Solute carrier organic anion transporter family member 1B1). A G at this location denotes the SLCO1B1*1B allele. among 8 healthy volunteers with *1B/*1B genotypes and 16 with the *1A/*1A genotype, *1B/*1B genotype associated with reduced plasma concentrations of repaglinide (but not nateglinide) consistent with increased hepatic uptake by SLCO1B1 (but w/ limited effects on nateglinide pharmacokinetics) news rs2306283 influences statin-related myopathy risk Genotyping panel for assessing response to cancer chemotherapy. Common variants in the SLCO1B3 locus are associated with bilirubin levels and unconjugated hyperbilirubinemia. Pazopanib-induced hyperbilirubinemia is associated with Gilbert's syndrome UGT1A1 polymorphism...
References:6
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[PharmGKB:Curated Subjects homozygous for this genotype showed decreased response to fluvastatin]
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Associated with periodontitis in a study of Chinese patients. rs2228570 aka rs10735810 allele (A) observed for breast cancer odds ratio (OR) of 1.26 Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity and osteoporosis. Patterns of linkage disequilibrium and haplotype distribution in disease candidate genes. Variants in the vitamin D receptor gene and asthma. Gene-environment interaction effects on the development of immune responses in the 1st year of life. Vitamin D receptor polymorphisms are associated with Graves' disease in German and Polish but not in Serbian patients. Asthma families show transmission disequilibrium of gene variants in the vitamin D metabolism and signalling pathway. Polymorphisms in the ...
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rs731236 protection from breast cancer (OR=0.80, 95%CI=0.64-0.99; p= 0.047) [PharmGKB:Curated This variant was significantly associated with acquired resistance to clodronate treatment in Caucasian patients with Paget's disease of the bone]
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Variants in the vitamin D receptor gene and asthma. Vitamin D receptor polymorphisms are associated with Graves' disease in German and Polish but not in Serbian patients. Asthma families show transmission disequilibrium of gene variants in the vitamin D metabolism and signalling pathway. Polymorphisms in the vitamin D receptor and their associations with risk of schizophrenia and selected anthropometric measures. Vitamin D pathway gene polymorphisms, diet, and risk of postmenopausal breast cancer: a nested case-control study. Optimization of candidate-gene SNP-genotyping by flexible oligonucleotide microarrays; analyzing variations in immune regulator genes of hay-fever samples. Vitamin D receptor gene (VDR) associations with cancer. Genome-wide association with bone mass and geometry in t...
Intermediate risk of low bone mineral density disorders
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rs1544410, also known as the BsmI polymorphism, is a SNP in the Vitamin D receptor (VDR). Multiple studies examining bone mineral density (BMD) in women have associated the A allele with increased risk of low BMD , , & . Additionally, A meta-analysis of 26 studies estimated a decreased risk of osteoporosis associated with the G;G genotype with an odds ratio of 0.61, 95% CI, 0.40-0.92 . rs1544410 increases susceptibility to Shorter stature for carriers of the A allele [PharmGKB:Curated This variant is associated with etidronate response in Caucasian (Slovenian) postmenopausal women (24 patients), with bb genotype associated with lower increase in bone mineral density (BMD) after bisphosphonate treatments.]
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[PharmGKB:In-Depth Associated with susceptibility to asthma and with IgE levels.]
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[PharmGKB:In-Depth Associated with susceptibility to asthma and bronchodilator response.]
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[PharmGKB:In-Depth Associated with response to bronchodilators]
Frequency: 33.6%
References:11
References:11
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Genome-wide association with bone mass and geometry in the Framingham Heart Study. Vitamin D receptor gene polymorphisms and epithelial ovarian cancer risk. CDX2 VDR polymorphism and colorectal cancer. Vitamin D receptor gene haplotypes and susceptibility to HIV-1 infection in injection drug users. Vitamin D receptor gene polymorphisms and haplotypes and postmenopausal breast cancer risk. Association of vitamin D receptor gene variants, adiposity and colon cancer. Modification of the inverse association between dietary vitamin D intake and colorectal cancer risk by a FokI variant supports a chemoprotective action of Vitamin D intake mediated through VDR binding. Circulating 25-hydroxyvitamin D, VDR polymorphisms, and survival in advanced non-small-cell lung cancer. Colon tumor mutations an...
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Association of single-nucleotide polymorphisms in JAK3, STAT4, and STAT6 with new cardiovascular events in incident dialysis patients. An association study of the signal transducer and activator of transcription 6 gene with periodic psychosis.
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rs4646(A) allele carriers with breast cancer being treated with letrozole are reported to do worse than rs4646(C;C) patients, based on a study of (only) 95 women. [PharmGKB:Curated A study in 67 patients with hormone receptor-positive metastatic breast cancer treated with letrozole, the presence of this SNP in the 3' untranslated region of the CYP19A1 gene is associated with improved treatment efficacy.]
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[PharmGKB:Curated Associations were found between LTC4S (rs730012) and LTA4H (rs2660845) and exacerbation rates in asthma patients treated with montelukast.] [OMIM:LEUKOTRIENE A4 HYDROLASE; LTA4H]
Frequency: 31.0%
References:1
References:1
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[GWAS:Response to cholinesterase inhibitors in Alzheimer's disease]
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In a survey that scanned 80 genes, no SNPs with a large effect were found to be associated with bipolar disorder. However, the SNP with the largest association was rs1170191, in first intron of the diacylglycerol kinase eta DGKH gene. The odds ratio for the risk allele of this SNP is 1.59 (p = 1.5x10e-8, experiment-wide p<0.01).
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[PharmGKB:Curated A sudy of 760 adult patients with moderate-to-severe depression, treated with escitalopram found that individuals carrying two minor alleles of rs9316233 variant in the HTR2A gene achieved an improvement that was on average 3.1 MADRS points more than individuals carrying two common alleles during escitalopram treatment. This explains 1.1% of variance (P=0.0016) of the response to escitalopram.]
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Genetic variation in the serotonin 2A receptor and suicidal ideation in a sample of 270 Irish high-density schizophrenia families.
higher risk for RA
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rs6313, also known as T102C, is part of a 4-SNP haplotype in the serotonin 2A receptor gene HTR2A that has been associated with rheumatoid arthritis in a study of 1800 European patients. The risk allele is rs6313(C). The overall risk for the haplotype CTCC of SNPs rs6311-rs1328674-rs6313-rs6314 is 1.68 (CI: 1.20 - 2.34, p = 0.02). Note: the orientation of rs1328674 in dbSNP is opposite that cited by this publication; therefore, with respect to dbSNP, the haplotype of risk as cited above is CACC rather than CTCC. see also gs108 and gs226 Polymorphisms in the serotonin receptor gene HTR2A are associated with quantitative traits in panic disorder. [PharmGKB:Curated Risk or phenotype-associated allele (s): T/T. Phenotype: Patients, with a diagnosis of probable Alzheimer's disease, carryi...
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Mutation analysis and the correlation between genotype and phenotype of Arg778Leu mutation in chinese patients with Wilson disease.
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Genetic polymorphisms in the nucleotide excision repair pathway and lung cancer risk: a meta-analysis. Explorative study to identify novel candidate genes related to oxaliplatin efficacy and toxicity using a DNA repair array. Cis-acting genetic variation at an E2F1/YY1 response site and putative p53 site is associated with altered allele-specific expression of ERCC5 (XPG) transcript in normal human bronchial epithelium.
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[OMIM:G30 GENE]
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[PharmGKB:Non-Curated GWAS Results: Whole genome association study identifies polymorphisms associated with QT prolongation during iloperidone treatment of schizophrenia (Initial Sample Size: 183 individuals; Replication Sample Size: NR; Risk Allele: rs7142881-A). This variant is associated with Response to iloperidone treatment (QT prolongation).] [GWAS:Response to iloperidone treatment (QT prolongation)]
normal
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rs17435 is one of several SNPs in the methyl CpG binding protein 2 (MECP2) that have been associated with risk for systemic lupus erythromatosis (SLE). The MECP2 gene is located on the X chromosome, which may be instructive since lupus is a predominantly female disease. An initial survey of 600 Korean patients, followed by 1,000 Caucasian patients, ultimately led to a meta-analysis indicating an odds ratio for the rs17435(T) risk allele of 1.39 (CI: 1.24–1.56, p = 1.2×10e-08). Variants within MECP2, a key transcription regulator, are associated with increased susceptibility to lupus and differential gene expression in patients with systemic lupus erythematosus. Replication of recently identified systemic lupus erythematosus genetic associations: a case-contro...
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[PharmGKB:Non-Curated GWAS Results: Whole genome association study identifies polymorphisms associated with QT prolongation during iloperidone treatment of schizophrenia (Initial Sample Size: 183 individuals; Replication Sample Size: NR; Risk Allele: rs4799915-T). This variant is associated with Response to iloperidone treatment (QT prolongation).] [GWAS:Response to iloperidone treatment (QT prolongation)]
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rs4149601 has been associated with hypertension. This SNP by itself was associated with diastolic blood pressure (DBP) (p=0.03) and DBP progression over time (p=0.04); in genotypic combination with intronic NEDD4L SNP rs2288774 it was associated with systolic blood pressure (SBP) (p=0.01), DBP (p=0.04), and progression of both SBP (p=0.03) and DBP (p=0.05) over time. Polymorphism in NEDD4L is associated with increased salt sensitivity, reduced levels of P-renin and increased levels of Nt-proANP. Expression, transcription, and possible antagonistic interaction of the human Nedd4L gene variant: implications for essential hypertension. Two polymorphisms in NEDD4L gene and essential hypertension in Chinese Hans - a population-based case-control study. Physiological interaction between alpha-ad...
None
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rs2108622 is a SNP in the cytochrome P450, family 4, subfamily F, polypeptide 2 CYP4F2 gene. In the males rs2108622(G) was significantly higher in cerebral infarction patients (P = 0.025) A study of Italian patients concluded that rs2108622(T;T) patients require 5.49 mg/day of warfarin versus 2.93 mg/day for (C;C) patients. Analysis of variance indicates that about 7% of mean weekly warfarin dose variance is explained by CYP4F2 genotype. A study of 370 Brazilian ('admixed') patients concludes that prospective CYP4F2 genotyping is of little value to these patients, presumably due to ethnic-based differences. [PharmGKB:Curated Risk or phenotype-associated allele: no allelic association. Phenotype: Improved pharmacogenetic algorithm-based warfarin dosing. Study size: 370. Study population/et...
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[GWAS:Capecitabine sensitivity]
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[PharmGKB:Curated Phenotype: This variant is associated with null virological response (NVR) in Janapese patients with hepatitis C virus infection treated with PEG-INF-alpha plus ribavirin. Study size: 304. Study population/ethnicity: Japanese. Significance metric(s): P=2.4 x 10(-29) (NVR). Type of association: GN; CO]
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[PharmGKB:Curated Phenotype: This variant is associated with null virological response (NVR) in Janapese patients with hepatitis C virus infection treated with PEG-INF-alpha plus ribavirin. Study size: Initial sample:154; Replication Sample: 172. Study population/ethnicity: Japanese. Significance metric(s): P=1.98 x 10(-31) (NVR). Type of association: GN; CO]
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[PharmGKB:Curated Phenotype: This variant is associated with null virological response (NVR) in Janapese patients with hepatitis C virus infection treated with PEG-INF-alpha plus ribavirin. Study size: Initial sample:154; Replication Sample: 172. Study population/ethnicity: Japanese. Significance metric(s): P=1.8 x 10(-30) (NVR). Type of association: GN; CO]
Frequency: 13.8%
References:9
References:9
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[PharmGKB:Curated Phenotype: This variant is associated with null virological response (NVR) in Janapese patients with hepatitis C virus infection treated with PEG-INF-alpha plus ribavirin. Study size: Initial sample:154; Replication Sample: 172. Study population/ethnicity: Japanese. Significance metric(s): P=2.84 x 10(-31) (NVR). Type of association: GN; CO]
Frequency: 8.8%
References:26
References:26
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23andMe blog rs8099917(C) less likely to respond to Hepatitis C treatment. rs12979860(C;C) better able to become naturally Hepatitis C virus-free. rs12980275(A) usually corresponds to the rs12979860(C) Variants in IL28B in liver recipients and donors correlate with response to peg-interferon and ribavirin therapy for recurrent hepatitis C. Importance of IL28B gene polymorphisms in hepatitis C virus genotype 2 and 3 infected patients. Predictive value of the IL28B polymorphism on the effect of interferon therapy in chronic hepatitis C patients with genotypes 2a and 2b. Peginterferon and ribavirin treatment for hepatitis C virus infection. IL28B polymorphisms predict reduction of HCV RNA from the first day of therapy in chronic hepatitis C. IL28B polymorphisms, IP-10 and viral load predict v...
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[PharmGKB:Curated Phenotype: Sequencing of the IL28B gene in 96 individuals found this SNP to be highly associated with rs12979860 (r - squared > 0.85), which, in a GWAS done in patients of European ancestry, African-Americans and Hispanics was significantly associated with rate of SVR (sustained virological response) to treatment of chronic Hepatitis C genotype I infection with peginterferon-alpha-2a or -2b combined with ribavirin.]
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CYP2B6 polymorphisms influence the plasma concentration and clearance of the methadone S-enantiomer.
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Pharmacokinetics of efavirenz when co-administered with rifampin in TB/HIV co-infected patients: pharmacogenetic effect of CYP2B6 variation. The pharmacokinetics and pharmacogenomics of efavirenz and lopinavir/ritonavir in HIV-infected persons requiring hemodialysis. Polymorphisms of drug-metabolizing enzymes (GST, CYP2B6 and CYP3A) affect the pharmacokinetics of thiotepa and tepa. The impact of cytokines on the expression of drug transporters, cytochrome P450 enzymes and chemokine receptors in human PBMC. Associations between CYP2B6 polymorphisms and pharmacokinetics after a single dose of nevirapine or efavirenz in African americans. CYP2B6 (c.516G-->T) and CYP2A6 (*9B and/or *17) polymorphisms are independent predictors of efavirenz plasma concentrations in HIV-infected patients. CYP...
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Associations between CYP2B6 polymorphisms and pharmacokinetics after a single dose of nevirapine or efavirenz in African americans. Univariate/multivariate genome-wide association scans using data from families and unrelated samples. CYP2B6 variants and plasma efavirenz concentrations during antiretroviral therapy in Port-au-Prince, Haiti. Tests of association for quantitative traits in nuclear families using principal components to correct for population stratification. Family-based bivariate association tests for quantitative traits. A comparative study of three methods for detecting association of quantitative traits in samples of related subjects. Family-based genome-wide association study for simulated data of Framingham Heart Study. The Genetic Analysis Workshop 16 Problem 3: simulat...
Magnitude: 1
References:4
References:4
Reduced CYP2A6 metabolism; impaired nicotine metabolism?
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rs28399433, also known as -47A>C, is a SNP in the CYP2A6 gene. CYP2B6 (c.516G-->T) and CYP2A6 (*9B and/or *17) polymorphisms are independent predictors of efavirenz plasma concentrations in HIV-infected patients. CYP2B6 variants and plasma efavirenz concentrations during antiretroviral therapy in Port-au-Prince, Haiti. [PharmGKB:In-Depth This variant results in decreased enzyme expression and activity, which affects nicotine and coumarin metabolism; part of the CYP2A6*9 haplotype.]
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rs2279343, also known as Lys262Arg, is a SNP within the CYP2B6 gene. variants including the Arg allele include CYP2B6*4, CYP2B6*6, and CYP2B6*7 Pharmacokinetics of efavirenz when co-administered with rifampin in TB/HIV co-infected patients: pharmacogenetic effect of CYP2B6 variation. Polymorphisms of drug-metabolizing enzymes (GST, CYP2B6 and CYP3A) affect the pharmacokinetics of thiotepa and tepa. Associations between CYP2B6 polymorphisms and pharmacokinetics after a single dose of nevirapine or efavirenz in African americans. CYP2B6 variants and plasma efavirenz concentrations during antiretroviral therapy in Port-au-Prince, Haiti. Cyclophosphamide-metabolizing enzyme polymorphisms and survival outcomes after adjuvant chemotherapy for node-positive breast cancer: a retrospective cohort s...
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Pleiotropic effects of GIP on islet function involve osteopontin. Genetic variation in the glucose-dependent insulinotropic polypeptide receptor modifies the association between carbohydrate and fat intake and risk of type 2 diabetes in the Malmo Diet and Cancer cohort. [PharmGKB:Curated Risk or phenotype-associated allele: A . Phenotype 1: In a meta-analysis of nine genome-wide association studies (n = 15,234 nondiabetic individuals) and a follow-up of 29 independent loci (n = 6,958-30,620), this SNP was found to be associated with 2-h glucose level (a clinical measure of glucose tolerance). Effect (s.e.m.) = 0.09(0.01) mmol/l per A allele. Study size/population/ethnicity: 15,234 plus 6,958-30,620 nondiabetic individuals of European descent. Significance metric(s): p = 1.98 x 10(-15). Ph...
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[GWAS:Ulcerative colitis]
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SNPs nominally associated with schizophrenia (rs3787283, rs3746544) were the same as those previously demonstrated to be associated with ADHD but with the opposite alleles, allowing the intriguing hypothesis that genetic variation at SNAP25 may be differentially associated with both schizophrenia and ADHD When comparing pooled results of multiple ADHD studies, only rs3746544(A) was found to have a significant association (p=0.028) with slightly increased risk (OR 1.15 at 95%) of ADHD. Support for the MnlI polymorphism of SNAP25; a Korean ADHD case-control study. Investigation of variation in SNAP-25 and ADHD and relationship to co-morbid major depressive disorder. Biased paternal transmission of SNAP-25 risk alleles in attention-deficit hyperactivity disorder.
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[PharmGKB:Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.000003; OR: 11.1 (2.5, 103.3)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.] [GWAS:Treatment response to TNF antagonists]
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[PharmGKB:Curated Risk or phenotype-associated allele: not stated Phenotype: Using a Quantitative Transmission Disequilibrium Test (QTDT), this variant was significantly associated with etoposide toxicity based upon IC50 values in cell lines from 30 parent-child trios. Study size: 176. Study population/ethnicity: 87 European descent Caucasians and 89 Yorubans. Significance metric(s): p = 0.00005. Type of association: FA; GN.]
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rs4810485 is a SNP associated with rheumatoid arthritis (RA), a chronic autoimmune disease characterized by joint inflammation. At this locus, the minor allele, T, protects against RA. The SNP is located on chromosome 20q13 in the second intron of the CD40 gene, which encodes a receptor that is expressed on the surface of multiple immune cells. CD40 binds the ligand CD154 which is expressed by activated T cells, and this interaction plays a critical role in T cell helper activity in the immune system. rs4810495 is closely linked with another SNP, rs1883832, that appears to lesson translation of the CD40 gene, affecting this critical signaling pathway that leads to B cell proliferation . Mouse model knockouts of CD40 have been shown to alleviate arthritis . The association between rs4810485...
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[PharmGKB:Curated Phenotype : In a meta-analysis of 21 GWAS cohorts followed by analysis in additional individuals, this SNP was found to be associated with fasting glucose level. Study size: 116,882. Significance metric(s): p = 6.6 x 10(-12). Study population/ethnicity: Non-diabetic Individuals of European descent. Type of association: CO;GN.] [GWAS:Fasting glucose-related traits]
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[GWAS:None]
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[GWAS:None]
References:2
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GPX1 Pro198Leu polymorphism, interactions with smoking and alcohol consumption, and risk for lung cancer. Gene x Gene interaction between MnSOD and GPX-1 and breast cancer risk: a nested case-control study. Genetic association of glutathione peroxidase-1 with coronary artery calcification in type 2 diabetes: a case control study with multi-slice computed tomography. Do genetic factors protect for early onset lung cancer? A case control study before the age of 50 years. A prospective study of genetic polymorphism in MPO, antioxidant status, and breast cancer risk. Oxidative response gene polymorphisms and risk of adult brain tumors. The Mn-superoxide dismutase single nucleotide polymorphism rs4880 and the glutathione peroxidase 1 single nucleotide polymorphism rs1050450 are associated with ...
Frequency: 23.0%
References:8
References:8
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[PharmGKB:Curated Lymphocytes carrying the C allele of the IMPDH2:IVS7+10T>C variant had less of a response to mycophenolic acid treatment compared to cells from TT individuals.]
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An in silico functional analysis using FASTSNP predicts that this rs4974081 (-3624 A/G) could be a potential transcription factor binding site. This finding suggests that rs4974081 could be a good candidate SNP for association studies with immunosuppressive and chemotherapeutic therapy outcomes.
1.2x increased risk for type-2 diabetes
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rs1470579 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.18 (CI: 1.07-1.31, p = 8.3 x 10e-4) T2D and normal glucose tolerant (NGT) individuals. (3,295 T2D and 3,595 NGT), strong associations with T2D were found for *CDKAL1 (OR(rs7756992) = 1.30[1.19-1.42], P = 2.3x10(-9)) *CDKN2A/2B (OR(rs10811661) = 0.74[0.66-0.82], P = 3.5x10(-8)) *IGFBP2 (OR(rs1470579) = 1.17[1.07-1.27], P = 0.0003) SNPs. T2D risk increased strongly when risk alleles, including the previously discovered T2D-associated TCF7L2 rs7903146 SNP, were combined (8.68-fold for the 14% of French individuals carrying 18 to 30 risk alleles with an allelic OR of 1.24) Neither rs4402960 or rs1470579 were found to be associated with type-2 diabetes in a study of 3,000 French Caucasi...
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rs167771 was significantly associated with autism spectrum disorder in a study of 144 patients. G allele associated with increased extra-pyramidal symptom risk as a result of risperidone treatment in a study of 321 psychiatric inpatients (81 presenting with EPS and 189 without) [PharmGKB:Curated Risk or phenotype-associated allele: G. Phenotype: The G variant of rs167771 was associated with increased risk for extrapyramidal symptoms in psychiatric patients receiving risperidone. Study size: 132. Study population/ethnicity: Patients with Schizophrenia or Bipolar disorder receiving antipsychotics; Caucasians; Spain; Catalonia. Significance metric(s): OR = 3.3; p = 0.00013. Type of association: PD.]
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Gene variants associated with deep vein thrombosis. Updated analysis of gene variants associated with deep vein thrombosis. Explaining variability in ciclosporin exposure in adult kidney transplant recipients. Polymorphisms in NF-kappaB, PXR, LXR, PPARgamma and risk of inflammatory bowel disease. Pregnane X receptor (PXR/NR1I2) gene haplotypes modulate susceptibility to inflammatory bowel disease. Variants of the human NR1I2 (PXR) locus in chronic periodontitis.
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Association of warfarin dose with genes involved in its action and metabolism. [PharmGKB:Curated Risk or phenotype-associated allele: G. Phenotype: The multimarker composed of rs2461823/A-rs7643645/G was significantly associated with severity of nonalcoholic fatty liver disease (NAFLD) (P<6.9x10, beta: 0.45). In univariate analysis rs7643645/G was significantly associated with fatty liver disease (P<0.04), with an odds ratio of 1.457 (95% confidence interval: 1.018-2.086). Study size: 290. Study population/ethnicity: 188 NAFLD patients with different stages of disease severity and 102 healthy individuals. Type of association: GN.]
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rs5182 (573C/T) is a SNP within the AGTR1 (Angiotensin II receptor type 1). among 4,096 hypertensive subjects, the CT/CC genotypes were associated with reduced risk of heart attack among those treated with ACE inhibitors [PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: Homozygotes for the minor allele (TT) had reduced HR for cardiac events while treated with perindopril. Study size: 8907. Study population/ethnicity: PERGENE study; EUROPA trial; European; White. Significance metric(s): p = 0.054. Type of association: CO]
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rs10935838, rs2046934, rs5853517, and rs6809699 venous thromboembolism lower risk of incident DVT/PE as compared to the reference haplotype H1 (odds ratio=0.50, 95% CI=0.27-0.93, p=0.028)
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rs10935838, rs2046934, rs5853517, and rs6809699 venous thromboembolism lower risk of incident DVT/PE as compared to the reference haplotype H1 (odds ratio=0.50, 95% CI=0.27-0.93, p=0.028) [PharmGKB:Curated This SNP was used to tag the H2 haplotype to show association with peripherial arterial disease and coronary artery disease.]
possible increased Alzheimer's risk
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The rs1803274(A) allele encodes a version of the butyrylcholinesterase enzyme known as the K variant; it may also be known as CHE*539T or BCHE*539T. The allele produces a 30% reduction in serum butyrylcholinesterase activity, and it is often co-inherited with the SNP encoding the so-called 'atypical' butyrylcholinesterase, rs1799807. Although not replicated by other studies, some studies have found, at least in certain populations, a possible association between this SNP and risk for Alzheimer's disease (independent of ApoE4 status): * reports ~2x increased Alzheimer's risk for carriers of one or more rs1803274(A) alleles, based on a study of 135 Canadian patients * reports ~3.5x increased Alzheimer's risk for carriers of one or more rs1803274(A) alleles, based on a study of 175 patients f...
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[PharmGKB:Curated Risk or phenotype-associated allele: C. Phenotype: This variant was associated with higher clearance of docetaxel. Study size: 31. Study population/ethnicity: Patients with Non-Small-Cell Lung Carcinoma. Significance metric(s): Type of association: PK.]
increased risk for heavy alcohol consumption
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http://www.scientificblogging.com/news_releases/comorbidity_ghrelin_hunger_hormone_implicated_in_alcohol_dependence Jörgen Engel, professor of pharmacology at the Sahlgrenska Academy, University of Gothenburg For this research, scientists recruited 417 Spanish individuals from the general population (n=279) as well as heavy drinkers (n=138) admitted to a hospital for treatment. The study sample – comprised of abstainers, moderate and heavy alcohol drinkers – was then examined for single nucleotide polymorphisms (SNPs) in the pro-ghrelin and growth hormone secretagogue receptors (GHS-R1A) (GHSR) gene. Findings showed that SNP rs2232165 of the GHS-R1A gene was associated with heavy alcohol consumption (and therefore presumably alcohol dependence). SNP rs2948694 of the same g...
References:1
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[OMIM:?]
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A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples. Polymorphisms in the VEGFA and VEGFR-2 genes and neovascular age-related macular degeneration. Genetic association of angiogenesis- and hypoxia-related gene polymorphisms with osteonecrosis of the femoral head. Pazopanib-induced hyperbilirubinemia is associated with Gilbert's syndrome UGT1A1 polymorphism. Association of polymorphisms/haplotypes of the genes encoding vascular endothelial growth factor and its KDR receptor with recurrent pregnancy loss.
References:2
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rs1047840, also known as K589E, is a SNP in the EXO1 gene. A study of 1,272 breast cancer Taiwanese patients concluded that the rs1047840(A) allele conferred a significantly (p=0.000025) increased risk of breast cancer.
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[GWAS:None]
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rs1367117 (C711T/711C>T) is a SNP within APOB (Apolipoprotein B). among 97 hypertensive subjects, C allele carriers responded to irbesartan with an average blood pressure reduction of 19 mmHg, however, they did not respond to atenolol associated with apoB levels [PharmGKB:Curated The APOB:711C>T, C allele was associated with reduction of blood pressure in response to irbesartan treatment but not atenolol treatment.] [OMIM:?] [GWAS:None]
metabolic consequences
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rs780094, a SNP in the GCKR gene encoding the glucokinase regulatory protein, contributes to the risk of type-2 diabetes and dyslipidaemia in mulitple populations. The effect on type 2 diabetes is probably mediated through impaired beta cell function rather than through obesity. The rs780094(A) risk allele is associated with the following traits : * higher levels of fasting serum triacylglycerol * impaired fasting and OGTT-related insulin release * dyslipidemia * somewhat reduced risk of type-2 diabetes There may also be an additive effect between this SNP and a SNP known as 'GCK -30A', rs1799884, at least on fasting serum insulin levels. rs780094 influences severe hypertriglyceridemia. 132 patients of European ancestry with severe HTG (fasting plasma TG>10 mmol/L), and 351 matched norm...
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rs1051740, also known as Tyr113His, is a SNP in the microsomal epoxide hydrolase EPHX1 gene. severe hypersensitivity syndrome, triggered by carbamazepine in the presence of a concomitant active human herpes virus (HHV) 6 and 7 infection with the allele HLA-A*3101 and rs1051740(C;C) [PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: In a logistic regression model adjusted for history of phenytoin use during the first trimester and maternal epilepsy, the maternal EPHX1 113 H (rs1051740 T/C) allele was associated with craniofacial abnormalities in the child. Study size: 157 pregnancies. Study population/ethnicity: phenytoin use during the first trimester and maternal epilepsy. metric(s): per rare allele OR: 2.43, 95% confidence interval (CI): 1.16-5.10, P=0.02. Type of asso...
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[PharmGKB:Curated Risk or phenotype-associated allele: undetermined. Phenotype: The variant allele was not associated with warfarin maintenance dose variability (p = 0.7223). Study size: 283. Study population/ethnicity: Hospitalized Caucasian patients aged 75 years or older, recruited Sep 2002-Nov 2004 in Ivry, France, and Oct 2005-Mar 2008 from 14 French centers. Significance metric(s): not significant. Type of association: GN; PK.]
1.9x risk for pre-eclampsia
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rs4762, a SNP in the angiotensin II AGT gene, has been reported to be associated with increased risk for developing pre-eclampsia, based on a study of ~180 French-Canadian women. The odds ratio associated with the rs4762(T) allele (encoding methionine) was 1.9 (CI:1.2–2.9, p=0.0033). Note that rs4762 is commonly referred to in the literature as 'T174M' or 'Thr174Met'; however, databases now indicate that the amino acid that varies is #207 (not 174), as the protein is currently numbered. rs4762 was also reported to play the major role in the 2.1 fold increased risk (CI: 1.4-3.4, p=0.0008) for pre-eclampsia of the rs3889728(A)-rs4762(T)-rs699(C) haplotype. Correction of population stratification in large multi-ethnic association studies. Ten renin-angiotensin system-relate...
increased risk for hypertension
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rs5051 is a SNP in the promoter of the angiotensin AGT gene, and presumably due to it's tight linkage with rs699, the rs5051(T) allele - as oriented to the dbSNP entry, not as published - has been associated with increased risk for hypertension and complications thereof. rs699(T) is associated with higher plasma angiotensinogen levels, and therefore the increased risk of essential hypertension. The frequency of the rs699(T) allele is also generally higher in African populations compared to Caucasian populations, correlating to the higher incidence of hypertension in African population. rs5051 is also known as 'A-6G'. For more details, see rs699. rs5051(T;T) homozygotes have been reported to be at increased risk for Crohn's disease, as based on one cohort of ~350 Australian patients. The od...
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An association analysis of Alzheimer disease candidate genes detects an ancestral risk haplotype clade in ACE and putative multilocus association between ACE, A2M, and LRRTM3. Disease-associated mutations that alter the RNA structural ensemble.
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[PharmGKB:Non-Curated GWAS Results: Newly identified loci that influence lipid concentrations and risk of coronary artery disease (Initial Sample Size: 8,656 individuals; Replication Sample Size: 11,399 individuals; Risk Allele: rs2144300-T). This variant is associated with HDL cholesterol levels.] [GWAS:Circulating myeloperoxidase levels (serum)] [GWAS:HDL cholesterol]
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Rs2237717 (major: C, minor: T) is located in intron 11 within the MET proto-oncogene. The MET gene is primarily known to be involved in tumor metastasis . However, MET has also been shown to have roles in general neurodevelopment and in the development of autism . Rs2237717 has been linked to schizophrenia, ability to recognize facial emotion, and chronic rhinosinusitis. ==Association with schizophrenia and cognitive ability== Given that schizophrenic patients have a lower incidence of cancer despite more exposure to risk factors and relatives without schizophrenia appear to also have a protective effect on cancer incidence, it has been hypothesized that alterations in cancer genes (like MET, containing rs2237717) may be involved in the pathogenesis of schizophrenia . ===Schizophrenia=== I...
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[PharmGKB:Curated Risk or phenotype-associated allele(s): G/G. Phenotype:the GG-genotype carriers were 2.5 times less likely to be overweight/obese (i.e. having a BMI above the 85th percentile). Study population/ethnicity: Children and adolescents, aged 7-17 years, treated with risperidone for 6 months or more.]
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[PharmGKB:Curated This intronic variant is moderately associated with olanzapine-induced median weight gain and significantly associated with extreme weight gain in schizophrenia subjects from north India.This variant alters the binding of a transcription factor (zinc finger 5) using in silico analysis.]
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[PharmGKB:Curated Risk or phenotype-associated allele: rs1801132 CC genotype. Phenotype: Increased prevalence of breast cancer in individuals with the combined genotypes of ESR1 rs1801132 CC and ERBB2 665 Ile/Val (rs1136201 A/C). Study size: 100 breast cancer patients (98 females) and 90 controls (84 females). Study population/ethnicity: Sudanese patients diagnosed between June 2004 and July 2005 in Khartoum. Significance metric(s): adjusted OR = 4.9; p = 0.05. Type of association: GN; CO.]
0.64x reduced lymphoma risk
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Associated with (reduced) risk for follicular lymphoma. Based on studying ~1,300 patients in 2 populations, for (C;C) homozygotes, the odds ratio was 0.42 (CI: 0.23-0.77), and for the (C;T) heterozygotes, 0.64 (CI: .46-.88), p(trend) = 4x10e-4. estrogen receptor-positive breast cancer risk (C) have an Odds Ratio (OR) = 1.05 [95% Confidence Intervals (CI) 1.02-1.09] relative to t-allele homozygotes, P= 0.004. [PharmGKB:Curated In a French study population, the C allele of this SNP, which is located in intron 4 of ESR1, was associated with increased incidence of type 2 diabetes (diabetes mellitus, type 2). The C allele of this SNP was associated with increased fasting plasma glucose levels in Swedish males, although there was no significant association in the Swedish cohort between this SNP...
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[PharmGKB:Curated Associated with several different conditions, particularly among women.]
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rs394581, a SNP cited to be associated with the risk of Rheumatoid Arthritis (RA), is situated on 6q25.3 in the 5' untranslated region of the TAGAP gene , which encodes the T-cell Activation Rho GTPase activating protein . This gene is highly expressed in immune cells such as B-lymphocytes, T-lymphocytes, dendritic cells, natural killer cells, and monocytes, yet its specific role in immune function is still unclear . Meta-analysis of GWAS in RA with validation in independent samples identified the TAGAP as an RA susceptibility locus . ==Rheumatoid Arthritis and Genetics== RA is an autoimmune disease that is characterized by chronic and systemic inflammation . At least half the variance in RA risk is estimated to be genetic based on family studies . A twin study with nationwide British and ...
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[PharmGKB:Curated Risk or phenotype-associated allele: C/C. Phenotype: This variant modulates the effect of the SLC47A1 rs2289669 polymorphism on the glucose lowering effect of metformin. In users with the SLC22A1 rs622342 CC genotype there was a significant association with change in HbA1c levels and the genetic variation at the SLC47A1 rs2289669 (G to A) polymorphism (-0.68; 95% CI: -1.06 to -0.30; P=0.005). The multiplicative interaction between these two genotypes was statistically significant (-0.52; 95% CI: -0.94 to -0.11; P=0.015). Study size: 98. Study population/ethnicity: Caucasian. metric(s): P=0.005. Type of association: GN.]
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[PharmGKB:Non-Curated Increased metformin uptake in transfected cells] [GWAS:Blood metabolite levels]
Frequency: 53.1%
References:4
References:4
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[PharmGKB:Non-Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.0000003; OR: 4.6 (1.8, 12.3)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.] [GWAS:Treatment response to TNF antagonists]
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rs4410790 and rs2470893 influences habitual caffeine consumption [GWAS:None]
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rs1800797, rs1800796 and rs1800795 have been shown to affect both the transcription and secretion of IL-6, to symptomatic distal interphalangeal osteoarthritis based on 535 women. the G alleles of two promoter single-nucleotide polymorphisms (SNP) G-597A and G-174C were more common among the subjects with symptomatic DIP OA than among those with no disease (p-values corrected for multiple testing 0.020 and 0.024). Also, the carriage of at least one G allele in these positions increased the risk of disease (p=0.006 and, p=0.008, respectively). Carrying a haplotype with the G allele in all three promoter SNPs increased the risk of symptomatic DIP OA more than four-fold (OR 4.45, p=0.001). Carriage of the G-G diplotype indicated an increased risk of both symmetrical DIP OA (OR 1.52 95% CI 1.0...
complex; see details
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rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. Studies on rs1800795 now include potential associations with heart disease, Kaposi's sarcoma, type-2 diabetes, stroke, obesity, Hodgkin's lymphoma, sudden ...
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[PharmGKB:Curated A study in 121 acutely psychotic patients with DSM-IV schizophrenia receiving treatment with typical antipsychotic medication alone or plus risperidone showed that this variant in the NEF3 gene was associated with early response to the medication.]
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[PharmGKB:Curated A study in 121 acutely psychotic patients with DSM-IV schizophrenia receiving treatment with typical antipsychotic medication alone or plus risperidone showed that this variant in the NEF3 gene was associated with early response to the medication.]
References:1
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[OMIM:INSULIN-LIKE GROWTH FACTOR-BINDING PROTEIN 3; IGFBP3]
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Common genetic variation in IGF1, IGFBP-1, and IGFBP-3 in relation to mammographic density: a cross-sectional study. Genetic determinants of circulating insulin-like growth factor (IGF)-I, IGF binding protein (BP)-1, and IGFBP-3 levels in a multiethnic population. Polymorphisms in the insulin like growth factor 1 and IGF binding protein 3 genes and risk of colorectal cancer. Transcription factor 7-like 2 polymorphism and colon cancer. IGF-1, IGFBP-1, and IGFBP-3 polymorphisms predict circulating IGF levels but not breast cancer risk: findings from the Breast and Prostate Cancer Cohort Consortium (BPC3). Colon tumor mutations and epigenetic changes associated with genetic polymorphism: insight into disease pathways. Altered transmission of HOX and apoptotic SNPs identify a potential common ...
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Kin-cohort estimates for familial breast cancer risk in relation to variants in DNA base excision repair, BRCA1 interacting and growth factor genes. IGF1 and IGFBP3 tagging polymorphisms are associated with circulating levels of IGF1, IGFBP3 and risk of breast cancer. Genetic variation in IGF1, IGF-1R, IGFALS, and IGFBP3 in breast cancer survival among Chinese women: a report from the Shanghai Breast Cancer Study. A common coding variant in CASP8 is associated with breast cancer risk. Common genetic variation in IGF1, IGFBP-1, and IGFBP-3 in relation to mammographic density: a cross-sectional study. Genetic determinants of circulating insulin-like growth factor (IGF)-I, IGF binding protein (BP)-1, and IGFBP-3 levels in a multiethnic population. Polymorphisms in the insulin like growth fact...
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per OMIM, Ma et al. (2005) found two different DDC haplotypes associated with nicotine dependence in African Americans and European Americans (with measures of smoking quantity [SQ], heaviness of smoking index [HSI], and the Fagerstrom test for ND [FTND]) *in African Americans, rs921451(T), rs3735273(G), rs1451371(T), rs2060762(G), all three measures sig. associated after correction for multiple testing *in European Americans, rs921451(T), rs3735273(G), rs1451371(T), rs3757472(G), which showed a sig. assoc. w/ the SQ and FTND score Addiction [OMIM:DOPA DECARBOXYLASE; DDC]
Frequency: 52.5%
References:2
References:2
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per OMIM, Ma et al. (2005) found two different DDC haplotypes associated with nicotine dependence in African Americans and European Americans (with measures of smoking quantity [SQ], heaviness of smoking index [HSI], and the Fagerstrom test for ND [FTND]) *in African Americans, rs921451(T), rs3735273(G), rs1451371(T), rs2060762(G), all three measures sig. associated after correction for multiple testing *in European Americans, rs921451(T), rs3735273(G), rs1451371(T), rs3757472(G), which showed a sig. assoc. w/ the SQ and FTND score [PharmGKB:Curated A study on 2037 smokers and non-smokers from 602 nuclear families of African- or European-American ancestry found first evidence for the involvement of DDC in the susceptibility to nicotine dependence. This variant in the DDC gene is part of t...
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per OMIM, Ma et al. (2005) found two different DDC haplotypes associated with nicotine dependence in African Americans and European Americans (with measures of smoking quantity [SQ], heaviness of smoking index [HSI], and the Fagerstrom test for ND [FTND]) *in African Americans, rs921451(T), rs3735273(G), rs1451371(T), rs2060762(G), all three measures sig. associated after correction for multiple testing *in European Americans, rs921451(T), rs3735273(G), rs1451371(T), rs3757472(G), which showed a sig. assoc. w/ the SQ and FTND score [PharmGKB:Curated A study on 2037 smokers and non-smokers from 602 nuclear families of African- or European-American ancestry found first evidence for the involvement of DDC in the susceptibility to nicotine dependence. This variant in the DDC gene is part of t...
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per OMIM, Ma et al. (2005) found two different DDC haplotypes associated with nicotine dependence in African Americans and European Americans (with measures of smoking quantity [SQ], heaviness of smoking index [HSI], and the Fagerstrom test for ND [FTND]) *in African Americans, rs921451(T), rs3735273(G), rs1451371(T), rs2060762(G), all three measures sig. associated after correction for multiple testing *in European Americans, rs921451(T), rs3735273(G), rs1451371(T), rs3757472(G), which showed a sig. assoc. w/ the SQ and FTND score [PharmGKB:Curated In a total of 2037 smokers and non-smokers from 602 nuclear families of African- or European-American ancestry, this SNP in the DDC gene was significantly associated with two of the three adjusted nicotine dependence measures in the European-A...
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[PharmGKB:Curated Associated with increased expression in vitro.]
Frequency: 37.5%
References:1
References:1
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No evidence for association between polymorphisms in GRM3 and schizophrenia.
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[PharmGKB:Curated In a study of 78 African American and 65 white patients diagnosed with schizophrenia or schizoaffective disorder, this SNP in the GRM3 gene was found to have significant associations with response to risperidone over 2-12 weeks in both African-American and white patients.]
increased risk of cannabis dependence, lower (normal) cancer risk '''Association between ABCB1 C3435T polymorphism and increased risk of cannabis dependence.''' (2009). Patients with cannabis dependence (n=40) had a significantly higher 3435C allele frequency (62.5% versus 43.8% respectively, P=0.017) and CC genotype (50% versus 20%, P=0.005, OR=4.00 [1.50-10.60). The CC genotype was independently associated with cannabis dependence. This is the first time a significant specific genetic marker has been shown in cannabis dependence. ABCB1 polymorphisms may alter Delta9THC distribution, its psychoactive effects and individual vulnerability to dependence.
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rs1045642, also known as C3435T, is a SNP located in the ABCB1 gene. It is often studied in conjunction with rs2032582. C3435T has been mentioned by: * A 'Silent' Polymorphism in the MDR1 Gene Changes Substrate Specificity (for example, to verapamil) * (R)-lansoprazole (Prevacid) concentrations are significantly increased in CYP2C19 extensive metabolizers with ABCB1 C3435T C allele. * In a Korean population, plasma concentrations of fexofenadine (Allegra) were 17% lower in 2677AA/3435CC subjects and 47% higher in the 2677TT/3435TT subjects compared to 2677GG/3435CC subjects. * In contrast, in this study no association was observed between the C3435T polymorphism and fexofenadine plasma or urine concentrations in a German Caucasian population. * A meta-analysis including 9 case-control stud...
normal. better response to atorvastatin. greater severity of delusions in male schizophrenics. '''Association study between the MDR1 gene and clinical characteristics in schizophrenia.''' (2014). Male schizophrenic carriers of the G allele of variant rs2032582 exhibit greater severity of delusions.
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rs2032582, also known as G2677T, is a nonsynonymous SNP located in exon 21 of the ABCB1 gene. G2677 is also known as Ala893Thr. It is often studied in conjunction with rs1045642. The rs2032582(T) variant allele yields a 2.6 fold higher risk of developing lung cancer, and in particular, the type of lung cancer called squamous cell carcinoma (CI 1.7-4.0, P < .001). There appears to be little gene dosage effect, since homozygous rs2032582(T;T) carriers shoulder almost all the risk (odds ratio 6.75 compared to (A;A) homozygotes, CI 3.0-15.2). This risk is also independent of an individual's history of smoking. A study of 98 methadone-maintaining patients concluded that the higher (>150 mg/day) and lower (< or =150 mg/day) methadone dose groups differed significantly in their rs1128503...
Frequency: 26.5%
References:3
References:3
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[PharmGKB:Non-Curated The AUCs of irinotecan, SN-38, SN-38 glucuronide, and APC are influenced by rs3740066, rs2306283, rs35605, rs10276036, and rs717620 .]
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[PharmGKB:Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.000006; OR: 3.6 (1.5, 9.3)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.]
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[PharmGKB:Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.000003; OR: 8.5 (2.6, 36.5)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.]
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[PharmGKB:Non-Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.000002; OR: 4.6 (1.8, 12.3)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.] [GWAS:Treatment response to TNF antagonists]
0.65x lower risk of ovarian cancer; higher risk of coronary heart disease in some studies; somewhat reduced PON catalytic efficiency
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rs662, also known as Q192R, is a SNP in the PON1 gene. It codes for amino acid 192 of the paraoxonase (PON) protein. Variants of this SNP affect PON catalytic efficiency and are correlated with Heart disease and trait-anxiety scores. The normal form, rs662(A), encodes a glutamine (Q), while the variant, rs662(G)), encodes an arginine (R). . While some populations show an association between this SNP and Heart disease, not all do. Perhaps the most striking finding was reported in Japanese patients with non-insulin dependent diabetes mellitus (NIDDM). NIDDM patients with either one or two rs662(G) alleles had a 9 fold higher risk of coronary heart disease compared with rs662(A;A) NIDDM patients. table of odds for cardiovascular disease outcomes 274 ovarian epithelial carcinoma cases and 452 ...
higher risk for heart disease, diabetic retinopathy
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The snp is suspected of being somewhat confused as an ambiguous flip, because the ReferenceAllele of T has a HapMap freq of 15% in CEU. Also notable is that dbSNP shows RefSNP Alleles: A/C/G/T, and other bits that don't quite fit. While the text below is still of use, it is likely that some of the conclusions are reversed. rs854560, also known as L55M, is a SNP in the PON1 gene. It codes for amino acid 55 (or 54, depending on the numbering) of the paraoxonase (PON) protein. Variants of this SNP affect levels of PON protein and mRNA and are correlated with Heart disease, aspects of Diabetes including diabetic retinopathy, and trait-anxiety scores. The apparently more favorable form, rs854560(T), encodes a methionine and lead to elevated levels of paraoxonase, which is generally a good thing...
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[GWAS:Paraoxonase activity]
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the T allele of SNP rs1617640 in the promoter of the EPO gene is significantly associated with Proliferative diabetic retinopathy (PDR) and end stage renal disease (ESRD). The EPO concentration in human vitreous body was 7.5-fold higher in normal subjects with the TT risk genotype than in those with the GG genotype. [PharmGKB:Curated SNP is significantly associated with proliferative diabetic retinopathy and end stage renal disease.] [OMIM:ERYTHROPOIETIN; EPO]
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[PharmGKB:Curated The G allele of this variant is more frequent in patients with major depressive disorders (MDD) than in controls in a study consisting of 188 Chinese MDD patients and 346 controls.]
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[PharmGKB:Curated The T allele of this variant is more frequent in patients with major depressive disorders (MDD) than in controls in a study consisting of 188 Chinese MDD patients and 346 controls.]
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Influences blood volume and platelet count Determinants of platelet count in humans. [PharmGKB:Curated GWAS results: A novel variant on chromosome 7Q22.3 associated with mean platelet volume, counts and function. (Initial Sample Size: 1,221 individuals; Replication Sample Size: 7,365 individuals); (Region: 7q22.3; Reported Gene(s): Intergenic; Risk Allele: rs342293-G); (p-value= 1E-24).This variant is associated with Mean platelet volume.] [GWAS:MPV]
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[OMIM:CHOLINERGIC RECEPTOR, MUSCARINIC, 2; CHRM2]
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[OMIM:CHOLINERGIC RECEPTOR, MUSCARINIC, 2; CHRM2]
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No significant association was found between this CHRM2 gene SNP and diverse measures of cognitive ability in two population based cohorts - one Scottish aged over 50 years (N = 2,091) and the other English comprising non-demented elderly participants (N = 758)- nor in a family-based Australian adolescent sample (N = 1,537). No evidence for association between 19 cholinergic genes and bipolar disorder. A genetic association analysis of cognitive ability and cognitive ageing using 325 markers for 109 genes associated with oxidative stress or cognition. Exploring the functional role of the CHRM2 gene in human cognition: results from a dense genotyping and brain expression study. Uncovering genes for cognitive (dys)function and predisposition for alcoholism spectrum disorders: a review of hum...
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QT interval rs3807375 rs2880058 [PharmGKB:Curated QT prolongation] [GWAS:Electrocardiographic traits]
None
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The NOS3 gene encodes nitric oxide synthase 3, and is also known as eNOS; rs2070744 is a SNP in the promoter region that is associated with higher levels of the corresponding mRNA (and possibly protein). Associations for the risk allele (C) of this SNP include: * Rheumatoid Arthritis , and, * cardiovascular mortality in high-risk patients * Progression (but not occurence) of prostate cancer Men who carry the C allele responded more favorably to the antihypertensive effects of aerobic exercise Current HapMap data for this SNP appears wrong (ss42994451). The population diversity information is instead being estimated based on ss48295994 P1, and should be replaced what a new HapMap ss# is available. [PharmGKB:Curated Risk or phenotype-associated allele: C. Phenotype: Subjects carrying the eN...
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[OMIM:?] [GWAS:Rheumatoid arthritis]
References:1
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rs1041983, also known as C282T, is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The allele associated with slow NAT2 metabolization for this SNP is rs1041983(T). Genosets gs154 and gs156 evaluate predicated NAT2 metabolizer phenotype based on rs1041983 and rs1801280. [PharmGKB:Curated in vitro study; PK: 22-fold reduction in Vmax vs wild type]
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[PharmGKB:Curated This variant is associated with triglyceride lowering response after fibrate treatment in patients with hypertriglyceridemia. Individuals with the G/G genotype had a significantly lower triglyceride lowering reponse than those with wild type.]
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Genetic variation in the dopamine pathway and smoking cessation.
normal
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rs1611115 (C-1021T) is a SNP near the dopamine beta-hydroxylase (DBH) gene. per OMIM, the T allele is associated with lower DBH expression in plasma (16 of TT genotype had DBH activity of 4.1, 46 of CT genotype had DBH activity of 25.2, and 112 of CC genotype had DBH activity of 48.1 nmol/min/ml) Association tests related to affective disorders such as ADHD were performed using four independent samples, healthy volunteers (N = 387), patients with affective disorders (N = 182), adult attention deficit hyperactivity disorder (ADHD) patients (N = 407), and patients with personality disorders (N = 637). Personality disorder patients carrying the DBH TT genotype exhibited higher neuroticism and novelty seeking scores as compared to individuals with the (C;C) or (C;T) genotype. Analyses on the l...
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a significant association between rs3924999 and Alzheimer's disease with psychosis [OMIM:NEUREGULIN 1; NRG1]
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http://papers.ssrn.com/sol3/papers.cfm?abstract_id=1915939 Born to Lead? A Twin Design and Genetic Association Study of Leadership Role Occupancy leadership role occupancy is associated with rs4950 residing on a neuronal acetylcholine receptor gene (CHRNB3). rs4950(G;G) less likely to be in a leadership role http://www.sciencedaily.com/releases/2013/01/130115111553.htm https://www.23andme.com/you/community/thread/16689/
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Linkage disequilibrium blocks, haplotype structure, and htSNPs of human CYP7A1 gene. Cholesterol 7alpha-hydrolase (CYP7A1) c.-278A>C promoter polymorphism in gallstone disease patients. CYP7A1 (-204 A>C; rs3808607 and -469 T>C; rs3824260) promoter polymorphisms and risk of gallbladder cancer in North Indian population. Promoter variant -204A > C of the cholesterol 7alpha-hydroxylase gene: association with response to plant sterols in humans and increased transcriptional activity in transfected HepG2 cells.
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[PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: The C allele was correlated with increased overall survival (CC vs. CT vs. TT: 15.4, 7.3, 4.8 months) given combined pemetrexed/bevacizumab treatment (p = 0.04), and lymphopenia as an adverse drug effect (p <= 0.05). Study size: from a study using 48 patients with metastatic or stage IIIB nonsquamous non-small-cell lung cancer patients. Significance metric(s): log-rank p = 0.04, p <= 0.05. Type of association: CO, GN]
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news rs4355801, was associated with a 20% increased risk of osteoporosis (significant at P=0.038). At least one copy of the risk allele (A) of rs4355801 was found in 79% of study participants. Participants carrying at least one copy of each risk allele -- 22% of the study population -- had a 50% increased risk of osteoporosis, which was significant at P=0.0026, and a 29% increased risk of osteoporotic fractures (significant at P=0.014). rs3736228 associated with decreased bone mineral density (p=6.3x10(-12) for lumbar spine and p=1.9x10(-4) for femoral neck) and an increased risk of both osteoporotic fractures (odds ratio [OR] 1.3, 95% CI 1.09-1.52, p=0.002) and osteoporosis (OR 1.3, 1.08-1.63, p=0.008). rs4355801 associated with decreased bone mineral density (p=7.6x10(-10) for lumbar spi...
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[GWAS:None]
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[PharmGKB:Curated Risk or phenotype-associated variant: A. Phenotype: The A/C/G haplotype at rs2228622-rs3780413-rs3780412 showed a significant association with atypical antipsychotic-induced obsessive compulsive symptoms. Study size: 94. Study population/ethnicity: Patients with schizophrenia receiving atypical antipsychotics; Asian; Korea. Significance metric(s): p = 0.04. Type of association: CO.]
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Polymorphisms in the glutamate transporter gene SLC1A1 and obsessive-compulsive symptoms induced by second-generation antipsychotic agents. [PharmGKB:Curated Risk or phenotype-associated variant: C. Phenotype: The A/C/G haplotype at rs2228622-rs3780413-rs3780412 showed a significant association with atypical antipsychotic-induced obsessive compulsive symptoms. Study size: 94. Study population/ethnicity: Patients with schizophrenia receiving atypical antipsychotics; Asian; Korea. Significance metric(s): p = 0.04. Type of association: CO.]
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Association testing of the positional and functional candidate gene SLC1A1/EAAC1 in early-onset obsessive-compulsive disorder. Association of the SLC1A1 glutamate transporter gene and obsessive-compulsive disorder. A haplotype containing quantitative trait loci for SLC1A1 gene expression and its association with obsessive-compulsive disorder. Family-Based Association Testing of OCD-associated SNPs of SLC1A1 in an autism sample. Polymorphisms in the glutamate transporter gene SLC1A1 and obsessive-compulsive symptoms induced by second-generation antipsychotic agents. [PharmGKB:Curated Risk or phenotype-associated variant: G. Phenotype: The A/C/G haplotype at rs2228622-rs3780413-rs3780412 showed a significant association with atypical antipsychotic-induced obsessive compulsive symptoms. Stud...
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associations with higher warfarin dose, namely, VKORC1-8191 (rs61162043, P = 0.0041) and 18786 in CYP2C9 (rs7089580, P = 0.035) independent of the previous associations with these genes
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Impact of genetic polymorphisms in CYP2C8 and rosiglitazone intake on the urinary excretion of dihydroxyeicosatrienoic acids. Role of cytochrome P450 2C8 and 2J2 genotypes in calcineurin inhibitor-induced chronic kidney disease. Cytochrome P450 2C8 pharmacogenetics: a review of clinical studies. [PharmGKB:Curated Risk or phenotype-associated allele: C. Phenotype: This variant was associated with reduced risk for neurotoxicity with paclitaxel treatment. Study size: 132. Study population/ethnicity: Patients with Neoplasms receiving paclitaxel; Spain. Significance metric(s): HR = 0.59 (0.36-0.94); p = 0.026. Type of association: PK; TOX.]
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[PharmGKB:Curated Alleles positive for this variant are designated CYP2C8*4. In in vitro experiments, the paclitaxel 6 alpha-hydroxylase acivity associated with CYP2C8*4 appeared lower than the wildtpe but the difference was not significant.]
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[GWAS:Response to serotonin reuptake inhibitors in major depressive disorder (plasma drug and metabolite levels)]
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[PharmGKB:Curated Risk or phenotype-associated allele: TT genotype Phenotype: Using a Quantitative Transmission Disequilibrium Test (QTDT), this variant was significantly associated with increased gene expression of WNT5 (P = 7 ? 10?8), and etoposide toxicity (P = 5 ? 10?5) based upon IC50 values in cell lines from 30 parent-child trios. In combination, rs278917, rs10061997, rs12190776, and rs9730073 were all significant predictors of etoposide IC50, and accounted for 40% of the etoposide IC50 variation in Yorubans. Study size: 89. Study population/ethnicity: 89 Yorubans. Significance metric(s): P = 5 ? 10?5. Type of association: FA; GN.]
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(T;T) associated with a higher risk of osteonecrosis of the jaw in am small study of multiple myeloma patients under bisphosphonate therapy [PharmGKB:Non-Curated This variant was associated with bisphosphonate-related osteonecrosis of the jaw (ONJ) in a GWAS study. Individuals homozygous for the T allele had an increased risk for developing ONJ.] [OMIM:MYELOMA, MULTIPLE] [GWAS:Osteonecrosis of the jaw]
References:3
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[PharmGKB:Curated Risk or phenotype-associated allele: T Phenotype: The CYP2C19*17 allele was associated with significantly increased metabolism of imipramine. Study size: 178 Study population/ethnicity: Psychiatric patients aged 18-65 with a score of greater than or equal to 17 on the Hamilton Rating Scale for Depression. Significance metric(s): p = 0.035 Type of association: PK]
References:1
Frequency: 27.4%
References:1
References:1
Repute:Bad
References:38
References:38
~1.3x increased risk for heart disease
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rs10757274 is a SNP located in chromosomal region 9p21; to date (2009), it is the strongest genetic predictor of early myocardial infarction (heart attack) discovered so far. SNPs in this region are also associated with increased risk of stroke, abdominal aortic aneurysm (AAA), and intracranial aneurysm. Based on a large (20,000+) study primarily of Caucasian females, it appears that on its own, this single SNP does not improve on the discrimination or classification of predicted heart disease risk achieved by traditional risk factors, high-sensitivity C-reactive protein, and a family history of premature myocardial infarction. rs10757274 and rs2383206 can double the risk of heart diseaseAbout one in every four Caucasians are thought to carry the gene variants. rs10757278] in the same regi...
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[PharmGKB:Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.0000005; OR: 4.9 (1.8, 14.0)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.]
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Lack of replication of genetic predictors for the rheumatoid arthritis response to anti-TNF treatments: a prospective case-only study. [PharmGKB:Non-Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.0000005; OR: 4.9 (1.8, 14.0)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.] [GWAS:Treatment response to TNF antagonists]
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[PharmGKB:Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.0000006; OR: 5.4 (1.9, 17.3)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.] [GWAS:Amyotrophic lateral sclerosis]
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Genetic risk factors for rheumatoid arthritis differ in Caucasian and Korean populations. Association of CD40 with rheumatoid arthritis confirmed in a large UK case-control study. Overlap of disease susceptibility loci for rheumatoid arthritis and juvenile idiopathic arthritis. Genetic variants in the prediction of rheumatoid arthritis. Investigation of rheumatoid arthritis susceptibility genes identifies association of AFF3 and CD226 variants with response to anti-tumour necrosis factor treatment. Endometriosis and autoimmune disease: association of susceptibility to moderate/severe endometriosis with CCL21 and HLA-DRB1. [PharmGKB:Non-Curated GWAS Results: Common variants at CD40 and other loci confer risk of rheumatoid arthritis (Initial Sample Size: 3,393 cases, 12,460 controls; Replic...
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Associated with bipolar disorder in individuals of African ancestry.
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[PharmGKB:Curated This study investigated aldosterone response to two antihypertensive drugs with the result that the existence of one or more variants in the KNG1gene influences interindividual variation in aldosterone response. SNP rs4686799 was associated in African-American and European-American responders to the diuretic (p=0.04 and p=0.07 respectively).]
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[PharmGKB:Curated This study investigated aldosterone response to two antihypertensive drugs with the result that the existence of one or more variants in the KNG1gene influences interindividual variation in aldosterone response. The SNPs rs5030062 and rs698078 were significantly associated in European-American responders to the diuretic (p=0.05 and p=0.01) and European-American responders to the angiotensin receptor blocker (p=0.04 and p=0.02).]
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Association of adiponectin gene variations with risk of incident myocardial infarction and ischemic stroke: a nested case-control study. Single nucleotide polymorphisms at the adiponectin locus and risk of coronary heart disease in men and women. Variants of the adiponectin and adiponectin receptor 1 genes and breast cancer risk. Common variants in the adiponectin gene (ADIPOQ) associated with plasma adiponectin levels, type 2 diabetes, and diabetes-related quantitative traits: the Framingham Offspring Study. Variants of the adiponectin (ADIPOQ) and adiponectin receptor 1 (ADIPOR1) genes and colorectal cancer risk. The association of SNPs in ADIPOQ, ADIPOR1, and ADIPOR2 with insulin sensitivity in a cohort of adolescents and their parents. Association of the adiponectin gene variations wit...
Frequency: 9.7%
References:8
References:8
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A study of 733 breast cancer cases for 10 SNPs concluded that the rs2241766(G;T) genotype, in combination with certain genotypes at rs1501299, was at reduced risk (odds ratio 0.61, CI: 0.46-0.80). After categorizing individuals by adiponectin signaling status, this study found that compared with high signalers, intermediate signalers had a 4.16-fold increase in breast cancer risk (CI: 0.49-35.19), and low signalers had a 6.56x higher breast cancer risk (CI: 0.78-54.89, p(trend) = 0.001). Adiponectin signaling status was assigned as follows: rs1501299(G,G) + rs2241766(T,T) = low signaler<br> rs1501299(G,T) + rs2241766(T,T) = low signaler<br> rs1501299(G,G) + rs2241766(G,T) = low signaler<br> rs1501299(T,T) + rs2241766(T,T) = intermediate signaler<br> rs1501299(G,T) +...
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[PharmGKB:Non-Curated GWAS results: Genome-wide Linkage and Association Anaylses to Identify Genes Influencing Adiponectin Levels: The GEMS Study. (Initial Sample Size: 997 cases, 989 controls; Replication Sample Size: NR); (Region: 3q27.3; Reported Gene(s): ADIPOQ; Risk Allele: rs6773957-A); (p-value= 0.00000005).This variant is associated with Adiponectin Levels.] [OMIM:?] [GWAS:Adiponectin Levels]
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Common variants in the adiponectin gene (ADIPOQ) associated with plasma adiponectin levels, type 2 diabetes, and diabetes-related quantitative traits: the Framingham Offspring Study. The association of SNPs in ADIPOQ, ADIPOR1, and ADIPOR2 with insulin sensitivity in a cohort of adolescents and their parents. Association of the adiponectin gene variations with risk of ischemic stroke in a Korean population.
Frequency: 15.4%
References:1
References:1
higher blood pressure if <50
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rs8192678 encodes a SNP also known as Gly482Ser; the (A) allele encodes the Ser. Some reports have linked this SNP to risk for hypertension and systolic blood pressure (SBP). However, a meta-analysis of 13,000+ individuals did not find any such association. However, gene-age interaction was apparent. For diastolic blood pressure (DBP), p(interaction)<0.0001; for systolic BP, p(interaction)=0.026. In younger individuals (<50yrs; n=2511) the rs8192678(A) allele was associated with higher DBP (p=4.2 x 10<sup>-12</sup>) and SBP (p=7.2 x 10<sup>-12</sup>), but no association was evident for individuals over 50yrs (n=5088). Analysis of PGC-1alpha variants Gly482Ser and Thr612Met concerning their PPARgamma2-coactivation function. PPARGC1A coding variation may initiat...
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Lack of replication of genetic predictors for the rheumatoid arthritis response to anti-TNF treatments: a prospective case-only study. [PharmGKB:Non-Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.000004; OR: 4.6 (1.8, 12.3)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.] [GWAS:Treatment response to TNF antagonists]
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preterm birth rs4696480 (T-16934A and Arg753Gln) and rs5743708) (Thr399Ile) earlier birth for infants carrying two (-16934TA/AA and 753ArgGln/GlnGln)
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[PharmGKB:Curated N=24 Korean; PK: UGT2B15*2/*2 group vs UGT215*1/*1 showed 0.58 lower systemic clearance of lorazepam; p less than 0.001] [OMIM:URIDINE DIPHOSPHATE GLYCOSYLTRANSFERASE 2 FAMILY, MEMBER B28; UGT2B28]
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rs7439366, also known as Y268H, is a SNP in the UGT2B7 gene encoding the 2B7 UDP-Glucuronosyltransferase, active primarily in the liver. The rs7439366(C) allele encodes a histidine (H) at amino acid 268, and the (T) allele encodes a tyrosine (Y). Most publications refer to the histidine as the wild-type (more common) allele. In a study of glucuronidation activity of human livers, rs7439366(T;T) individuals had 28% lower activity than rs7439366(C;C) individuals with respect to O-glucuronidation of tamoxifen metabolites 4-OH-tamoxifen and endoxifen. The authors suggest this may help explain interindividual variability (beyond CYP2D6 variation) in tamoxifen metabolism - and therefore the effectiveness of tamoxifen in reducing breast cancer recurrence. [PharmGKB:Curated Risk or phenotype-asso...
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[GWAS:Obesity-related traits]
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Gemcitabine and arabinosylcytosin pharmacogenomics: genome-wide association and drug response biomarkers. [PharmGKB:Curated Risk or phenotype-associated allele: None. Phenotype: Variants identified in a screen of 13 genes involved in the gemcitabine drug metabolic pathway. For the intronic DCK:IVS1-1110T>C SNP, the C allele was not observed among the Europeans and Africans interrogated in this study. There was no significant difference between ethnic groups in genotype frequency distribution (p > 0.05). Study size: 179. Study population/ethnicity: Healthy, unrelated blood donors of European (n = 90) and African (n = 89) descent. Significance metric(s): Not significant, p > 0.05. Type of association: GN.]
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[GWAS:None]
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23andMe blog blood pressure High Blood Pressure (Hypertension) [GWAS:Diastolic Blood Pressure]
Frequency: 18.6%
References:7
References:7
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[PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: This SNP was associated with increased risk of myelosuppression in cancer patients treated with irinotecan. Study size: 108. Study population/ethnicity: Japanese patients with neoplasms; Japan. Significance metric(s): p = 0.036. Type of association: PK; CO.]
Frequency: 24.6%
References:6
References:6
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Gene expression and association analyses of LIM (PDLIM5) in bipolar disorder and schizophrenia. A polymorphism in the PDLIM5 gene associated with gene expression and schizophrenia. Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study. Positive association between PDLIM5 and schizophrenia in the Chinese Han population. A major single nucleotide polymorphism of the PDLIM5 gene associated with recurrent major depressive disorder. PDLIM5 and susceptibility to bipolar disorder: a family-based association study and meta-analysis. A case-control association study of the PDLIM5 gene and bipolar disorder in a Sardinian sample.
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A polymorphism in the PDLIM5 gene associated with gene expression and schizophrenia. Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study. Positive association between PDLIM5 and schizophrenia in the Chinese Han population. A case-control association study of the PDLIM5 gene and bipolar disorder in a Sardinian sample.
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dbSNP says its multiallelic and on the minus strand. In 23andMe results T is reference and C is minor. rs698 is also known as Ile350Phe, and is a SNP in the alcohol dehydrogenase 1C ADH1C gene. The rs698(A) allele is the more common, encoding the amino acid isoleucine (Ile); the quite rare rs698(T) allele encodes the variant phenylalanine (Phe). On it's own, this SNP is said to explain 12.3% of the variability in the rate at which alcohol is metabolized, based on a study of 250 Spaniards. More significantly (in a statistical sense), this study concluded that combinations of this SNP and others were shown to affect alcohol metabolism; most of these combinations are represented by the gs211 genoset. Note that the effects of alcohol are higher in individuals who break down (basically, detoxif...
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ADH single nucleotide polymorphism associations with alcohol metabolism in vivo.
Frequency: 14.3%
References:1
References:1
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[GWAS:Major depressive disorder]
Frequency: 30.1%
References:9
References:9
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Plasma complement components and activation fragments: associations with age-related macular degeneration genotypes and phenotypes. Genetic analysis of typical wet-type age-related macular degeneration and polypoidal choroidal vasculopathy in Japanese population. [OMIM:MACULAR DEGENERATION, AGE-RELATED, 1; ARMD1] [GWAS:Age-related macular degeneration]
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[GWAS:None]
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rs1799883 Fatty acid binding protein 2 (FABP2) Ala54Thr; The derived allele at SNP (A54T), rs1799883, in FABP2 increases strongly with latitude (p < 0.01) and may influence weight management Identification of four gene variants associated with myocardial infarction. Association of genetic variants with atherothrombotic cerebral infarction in Japanese individuals with metabolic syndrome. Association of genetic variants with chronic kidney disease in Japanese individuals with type 2 diabetes mellitus. Development of a fingerprinting panel using medically relevant polymorphisms. Soluble fibre (Plantago ovata husk) reduces plasma low-density lipoprotein (LDL) cholesterol, triglycerides, insulin, oxidised LDL and systolic blood pressure in hypercholesterolaemic patients: A randomised trial. ...
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[GWAS:None]
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association of the rs7483 SNP with late-onset Alzheimer's disease
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[PharmGKB:Curated This SNP at chromosome 2 is significantly associated with CYP1B1 expression (located on chromosome 2), and daunorubicin IC50 in CEU population using International HapMap cell lines.]
slightly less drug dependence, decreased effectiveness of analgesics
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Genome-wide association study identifies a potent locus associated with human opioid sensitivity rs2952768(C) was associated with more analgesic requirements ... exhibited less vulnerability to severe methamphetamine or alcohol dependence, fewer eating disorders, and a lower ‘Reward Dependence’ score on a personality questionnaire. The (C;C) genotype was significantly associated with the elevated expression of a neighboring gene, CREB. SNPs in this locus are the most potent genetic factors associated with human opioid sensitivity known to date, affecting both the efficacy of opioid analgesics and liability to severe substance dependence. Our findings provide valuable information for the personalized treatment of pain and drug dependence. [GWAS:Opioid sensitivity]
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[GWAS:Plasma homocysteine levels (post-methionine load test)]
Frequency: 26.5%
References:3
References:3
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[GWAS:None]
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[PharmGKB:Curated UGT1A7:-57T>G increases risk of anemia in irinotecan-treated patients.]
References:6
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Clinically relevant UGT1A10 variant.
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The (C;C) genotype is linked to reduced UGT1A1 activity, and increased Bilirubin, except in people of African origin for whom the T allele is a risk factor for breast cancer. [Genetic polymorphisms of MPO, NQO1, GSTP1, UGT1A6 associated with susceptibility of chronic benzene poisoning]. The influence of metabolic gene polymorphisms on urinary 1-hydroxypyrene concentrations in Chinese coke oven workers. Low-penetrance alleles predisposing to sporadic colorectal cancers: a French case-controlled genetic association study. [Relationship between genetic polymorphisms of phase I and phase II metabolizing enzymes and DNA damage of workers exposed to vinyl chloride monomer]. Serum bilirubin levels on ICU admission are associated with ARDS development and mortality in sepsis. Pazopanib-induced hyp...
References:6
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Clinically relevant UGT1A10 variant. [PharmGKB:Curated *93 is a common variant of UGT1A1 in Caucasian and African-American populations. It is located in the Phenobarbital Response Enhancer Module (an upstream regulatory sequence) and may be important in predicting irinotecan response.]
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PPARG by dietary fat interaction influences bone mass in mice and humans. Joint effect of peroxisome proliferator-activated receptor gamma genetic polymorphisms and estrogen-related risk factors on breast cancer risk: results from a case-control study in Taiwan. Variants of the human PPARG locus and the susceptibility to chronic periodontitis. Association of peroxisome proliferator-activated receptor gamma polymorphisms with inflammatory bowel disease in a Hungarian cohort.
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Associated with risk of lung cancer in a Chinese population
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rs2228001, also known as Lys939Gln, K939Q, and K940Q, is a SNP in the DNA nuclear excision repair gene xeroderma pigmentosum complementation group C XPC gene. The Lys (K) allele is encoded by the rs2228001(A) allele. A meta-analysis of 16 studies with 6797 cancer cases and 9018 controls concluded that rs2228001(C;C) homozygotes had an increased overall cancer risk (odds ratio of 1.16, CI: 1.05-1.28) compared with (A;A) homozygotes. This was primarily a risk for lung cancer. [PharmGKB:Curated Risk or phenotype-associated allele: Not specified. Phenotype: This SNP was associated with clearance of docetaxel. Study size: 31. Study population/ethnicity: Patients with Non-Small-Cell Lung Carcinoma. Significance metric(s): p = 0.0045 (ANOVA); p = 0.052 (QMIS); p = 0.0004 (KW) Type of association...
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rs1805124, also known as His558Arg or H558R, is a SNP in the cardiac sodium channel SCN5A gene. This SNP is quite common, a variants go, with an allele frequency of 10 - 25% in many populations. It seems to be considered to be a benign change. [PharmGKB:In-Depth Has been studied in association with long QT.] [OMIM:SODIUM CHANNEL, VOLTAGE-GATED, TYPE V, ALPHA SUBUNIT; SCN5A]
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colorectal cancer (-93G>A, rs1800734) 1,518 patients with CRC, homozygosity for the MLH1 -93A variant was associated with a significantly increased 3-fold risk of CRC negative for MLH1 protein by immunohistochemistry (odds ratio (OR): AA vs GG = 3.30, 95% CI 1.46-7.47, n = 1392, p = 0.004, MLH1 negative vs MLH1 positive CRC) and with a 68% excess of proximal CRC (OR: AA vs GG=1.68, 95% confidence interval (CI) 1.00-2.83, n = 1,518, p = 0.05, proximal vs distal CRC) [PharmGKB:Curated This promoter variant is a risk allele for the development of cancer after methylating chemotherapy for Hodgkin lymphoma.] [OMIM:MutL, E. COLI, HOMOLOG OF, 1; MLH1]
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rs2193225 has been reported to be associated with increased risk for nicotine dependence. [PharmGKB:Curated A study on 2037 individuals from 602 nuclear families of African-American or European-American origin found a significant associations of this SNP in the NRXN1 gene with smoking quantity, the heaviness of smoking index and the Fagerstr?m test for nicotine dependence in the European-American sample.]
References:1
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[GWAS:None]
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rs6721498 has been reported to be associated with increased risk for nicotine dependence. [PharmGKB:Curated A study on 2037 individuals from 602 nuclear families of African-American or European-American origin found a significant associations of this SNP in the NRXN1 gene with smoking quantity, the heaviness of smoking index and the Fagerstr?m test for nicotine dependence in the African-American sample.]
Frequency: 32.8%
References:1
References:1
References:1
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[PharmGKB:Curated The G allele of this SNP is associated with increased incidence of medium-severe nausea or vomiting, and with reduced leukocyte counts in gastric carcinoma and colon carcinoma patients treated with 5-fluorouracil. The elimination constant (Ke) for 5-fluorouracil was significantly lower in patients homozygous for the G allele.]
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age related macular degeneration [OMIM:COMPLEMENT FACTOR H-RELATED 3; CFHR3] [GWAS:Age-related macular degeneration]
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linked to blindness in age related macular degeneration rs3753394, rs800292, rs1061147, rs1061170, rs380390, and rs1329428 Significant associations were detected for AMD with rs3753394 rs800292 rs1329428 A haplotype of rs1061170 rs3753394 rs800292 rs1329428 (TGTC) was found to confer a significantly increased likelihood of exudative AMD CFH variations appear to contribute to ARMD in Caucasians, but not in Japanese [GWAS:None]
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[GWAS:Coronary artery disease]
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[PharmGKB:Curated Risk or phenotype-associated allele: TT genotype. Phenotype: In AML patients receiving cytarabine, the TT genotype for rs532545 was associated with decreased 5-year overall survival (13%) relative to the CC genotype (25%) (p = 0.05), and significantly higher lactate dehydrogenase levels relative to the CC and CT genotypes (p = 0.01). Patients with the TT genotype had greater than 50% increased risk for death compared with patients with the CC genotype (HR = 1.56, p = 0.02). Study size: 360. Study population/ethnicity: AML patients. /Caucasian Germans. Significance metric(s): Type of association: GN; CO; PD; TOX; ADR]
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[PharmGKB:Curated Risk or phenotype-associated allele: undetermined. Phenotype: The variant allele was not associated with warfarin maintenance dose variability (p = 0.7024). Study size: 283. Study population/ethnicity: Hospitalized Caucasian patients aged 75 years or older, recruited Sep 2002-Nov 2004 in Ivry, France, and Oct 2005-Mar 2008 from 14 French centers. Significance metric(s): not significant. Type of association: GN; PK.]
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[GWAS:None]
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[GWAS:Rheumatoid arthritis]
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rs231775, also known as +49A/G, is a SNP in the CTLA4 gene. which is linked to Hashimoto thyroiditis In a meta-analysis of CTLA4 gene SNPs, rs231775 was most associated with vitiligo; however, the association seems to hold only in the subgroup of patients with other autoimmune diseases. rs231775 (CTLA4_+49_G/A P=0.0219) and rs733618 (CTLA4_-1722_T/C P=0.0096) susceptibility to Graves' disease associated with the development of placental abruption and preeclampsia, with women having the G allele being at risk rs231775 was not associated with type-1 diabetes in a study of 207 Portuguese patients. [PharmGKB:Curated This SNP affects risk for Autoimmune Thyroid Disorder (AITD). The G allele is generally thought to be the risk-conferring allele, but this study found that which allele confers ri...
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Imputation-based analysis of association studies: candidate regions and quantitative traits. Genetic variants and susceptibility to neurological complications following West Nile virus infection.
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[PharmGKB:Curated A study on 50 subjects (25 patients who developed a distinct hearing loss during cisplatin therapy and in 25 patients without hearing impairment after cisplatin therapy)observed a higher frequency of the A-allele of rs2075252 in the LRP2 in the group with hearing impairment than in the group with normal hearing after cisplatin therapy.]
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Genetic predictors of the maximum doses patients receive during anti-epileptic drugs carbamazepine and phenytoin Possible commercial test [PharmGKB:Curated This SNP is associated with required dose levels of antieptilectic drugs. It affects alternative splicing and hence the proportions of neonate and adult alternative transcripts of SCN1A in adult brain tissue. The effect of the polymorphism appears to be modified by Nova2 expression levels.] [OMIM:SODIUM CHANNEL, NEURONAL TYPE I, ALPHA SUBUNIT; SCN1A]
References:1
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[PharmGKB:Curated This SNP on chromosome 1 was associated with the susceptibility to daunorubicin-induced cytotoxicity in the YRI population using International HapMap cell lines.]
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obesity Q223R rs1137101 may be associated with obesity in women with a psychotic disorder treated with atypical antipsychotic drugs Gln223Arg polymorphism could be considered a disease susceptibility modulating factor both in ischemic heart disease or dilated cardiomyopathy patients. [OMIM:LEPTIN RECEPTOR POLYMORPHISM]
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The IL10 C627A polymorphism in the anti-inflammatory Interleukin 10 gene decreases gene transcription. Effect of Interleukin-10 Gene Polymorphisms on Clinical Outcome of Patients with Aggressive Non-Hodgkin's Lymphoma. An exploratory study with negative results. rs1800872(A) carriers were 3x more likely to have their pregnancies terminate early (<10 weeks) than (C) carriers, based on a study of ~500 pregnancies. Gene-environment interaction effects on the development of immune responses in the 1st year of life. Cytokine polymorphisms in the Th1/Th2 pathway and susceptibility to non-Hodgkin lymphoma. Asthma families show transmission disequilibrium of gene variants in the vitamin D metabolism and signalling pathway. The interferon gamma gene polymorphism +874 A/T is associated with...
Normal prostate cancer risk
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This SNP is upstream of the IL10 gene, and is also known as the -1082G>A IL10 SNP. Dust mite exposure modifies the effect of functional IL10 polymorphisms on allergy and asthma exacerbations. Dust mite exposure significantly modified the relation between 3 SNPs in IL10 (rs1800896, rs3024492, and rs3024496). Homozygosity for the minor allele of each of the 3 SNPs was associated with increased risk of occurrence ( approximately 3-fold to 39-fold increase). A study of 258 prostate cancer cases concluded that the rs1800896(A) allele, known to result in lower levels of this anti-inflammatory cytokine, was positively associated with risk (AG vs. GG, odds ratio of 1.69, CI: 1.10-2.60; AA vs. GG, OR of 1.81, CI: 1.11-2.96).
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[PharmGKB:Curated This variant is associated with enhanced agonist-induced platelet aggragation and response to aspirin in both whites and african americans. The C allele was associated with increased aggregation of native platelets to collagen, epinephrine. The C allele was also associated with reduced platelet responsiveness to aspirin. (N=1486)]
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[PharmGKB:Non-Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.000005; OR: 10.2 (2.6, 59.2)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.] [GWAS:Treatment response to TNF antagonists]
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Lack of replication of genetic predictors for the rheumatoid arthritis response to anti-TNF treatments: a prospective case-only study. [PharmGKB:Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.00003; OR: 5.5 (1.8, 20.2)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.]
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[GWAS:Capecitabine sensitivity]
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Nicotine Dependence the minor allele of rs2072660 increased the mean score
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Polymorphisms within the C-reactive protein (CRP) promoter region are associated with plasma CRP levels. Genetic variation is associated with C-reactive protein levels in the Third National Health and Nutrition Examination Survey. Common variants in the CRP gene in relation to longevity and cause-specific mortality in older adults: the Cardiovascular Health Study. C-reactive protein (CRP) gene polymorphisms, CRP levels, and risk of incident coronary heart disease in two nested case-control studies. Genetic determinants of basal C-reactive protein expression in Filipino systemic lupus erythematosus families. Fine-mapping the genetic basis of CRP regulation in African Americans: a Bayesian approach. C-reactive protein, interleukin-6, and prostate cancer risk in men aged 65 years and older. I...
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[PharmGKB:Curated This variant is associated with differential antipsychotic treatment response in individuals of african descent. Patient with rs2842030 TT genotype responded better to perphenazine treatment than by quatiapine, risperidone or ziprasidone. Patient with European descent and rs2842030 GG genotype responded better to risperidone than those with TT genotype.No association was found between this variant and increased susceptibility to the etiology of schizophrenia in Han Chinese.]
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FcepsilonRIalpha gene (FCER1A) promoter polymorphisms and total serum IgE levels in Japanese atopic dermatitis patients.
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[PharmGKB:Curated lower response allele: C; phenotype: change in interocular pressure; study size: 100; study population: healthy Japanese subjects with no history of eye disease; description: change in interocular pressure: CC, 20.3%±1.5%; CT + TT, 15.6%±1.2%; P = 0.0316; T allele associate with lower transcriptional activity; type of association: CO]
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[PharmGKB:Curated This variant is associated with success rate of smoking cessation. Individuals carrying the minor allele have substantially decreased odds of quitting (OR = 0.31; 95% CI 0.18-0.55). This variant is in the 3' UTR region of CHRNB2 genes, and may have a role in the time to relapse and an impact on withdrawal symptoms at target quit date.]
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rs1042114 increases susceptibility to Substance dependence, Opioid 3.56 times for carriers of the G allele [OMIM:OPIOID RECEPTOR, DELTA-1; OPRD1]
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obesity and type-2 diabetes *rs1121980 *rs7498665 *rs4752856 *rs17782313 *rs2815752 *rs10938397 Is the thrifty genotype hypothesis supported by evidence based on confirmed type 2 diabetes- and obesity-susceptibility variants? Common body mass index-associated variants confer risk of extreme obesity. Novel obesity risk loci do not determine distribution of body fat depots: a whole-body MRI/MRS study. From monogenic to polygenic obesity: recent advances. A strategy for analyzing gene-nutrient interactions in type 2 diabetes. Obesity and diabetes genes are associated with being born small for gestational age: results from the Auckland Birthweight Collaborative study. FTO and MC4R gene variants are associated with obesity in polycystic ovary syndrome. Genetic predictors of weight loss and weig...
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[PharmGKB:Curated Risk or phenotype-associated allele: None. Phenotype: Variants identified in a screen of 13 genes involved in the gemcitabine drug metabolic pathway. For the non-synonymous CDA:79A>C (K27Q) SNP, the C allele (27Gln) was at frequency 0.36 and 0.04 in Europeans and Africans, respectively. There was a significant difference between ethnic groups in genotype frequency distribution (p < 0.001) Study size: 180. Study population/ethnicity: Healthy, unrelated blood donors of European (n = 95) and African (n = 85) descent. Significance metric(s): p < 0.001. Type of association: GN.]
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[GWAS:None]
Frequency: 54.0%
References:6
References:6
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per the 23andMe blog, the minor allele of this SNP (A) was associated with decreased cholesterol and triglycerides {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [PharmGKB:Non-Curated GWAS results: Loci influe...
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The SULT1C2: rs1402467 G variant was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0083 Type of association: PD; CO]
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associated with ankylosing spondylitis risk of Helicobacter pylori infection. Children carrying IL1A-889T had a lower risk of H. pylori positivity, compared to those carrying -889C, with each T allele associated with 43% risk reduction (OR = 0.57, 95% CI = 0.33-0.99, p-trend = .05) upregulation of pro-inflammatory cytokines may protect against persistent H. pylori colonization. Association study of functional genetic variants of innate immunity related genes in celiac disease. Prognostic significance of host immune gene polymorphisms in follicular lymphoma survival. Association of common polymorphisms in inflammatory genes with risk of developing cancers of the upper aerodigestive tract. Potential influence of IL1B haplotype and IL1A-IL1B-IL1RN extended haplotype on hand osteoarthritis ris...
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New atypical antipsychotics for schizophrenia: iloperidone. [PharmGKB:Non-Curated GWAS Results: Whole genome association study identifies polymorphisms associated with QT prolongation during iloperidone treatment of schizophrenia (Initial Sample Size: 183 individuals; Replication Sample Size: NR; Risk Allele: rs993648-T). This variant is associated with Response to iloperidone treatment (QT prolongation).] [GWAS:Response to iloperidone treatment (QT prolongation)]
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rs1801262 increases susceptibility to Type II Diabetes 1.15 times for carriers of the A allele Mutation of CERKL, a novel human ceramide kinase gene, causes autosomal recessive retinitis pigmentosa (RP26). NeuroD1 gene and interleukin-18 gene polymorphisms in type 1 diabetes in Dalmatian population of Southern Croatia. Identification of type 2 diabetes-associated combination of SNPs using support vector machine.
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rs1741981 and rs2547547 influence risk for postoperative hepatocellular carcinoma tumor recurrence up to 2.2x Detection of fetomaternal genotype associations in early-onset disorders: evaluation of different methods and their application to childhood leukemia.
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[GWAS:Age-related macular degeneration]
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[PharmGKB:Curated The T/T genotype of this SNP was associated with reduced risk of edema resulting from treatment with muraglitazar (BMS-298585) relative to the C/C genotype. The test population consisted of patients with diabetes or hyperlipidemia.]
Frequency: 49.6%
References:6
References:6
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[OMIM:COMPLEMENT FACTOR H-RELATED 3; CFHR3] [GWAS:None]
Frequency: 48.7%
References:9
References:9
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[OMIM:COMPLEMENT FACTOR H-RELATED 3; CFHR3] [GWAS:Age-related macular degeneration]
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[PharmGKB:Curated Risk or phenotype-associated allele: T Phenotype: The SPG7:rs2292954 T variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0004 Type of association: CO; TOX]
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The SPG7:rs12960 G variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.004 Type of association: CO; TOX]
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[GWAS:Type 2 diabetes]
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Single nucleotide polymorphisms of microRNA machinery genes modify the risk of renal cell carcinoma. Genetic variations in microRNA-related genes are novel susceptibility loci for esophageal cancer risk. Black carbon exposures, blood pressure, and interactions with single nucleotide polymorphisms in MicroRNA processing genes.
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rs1045280(T) associated with tardive dyskinesia in Chinese patients with schizophrenia (OR(T) = 1.58, 95% CI = 1.14-2.19, P = 0.007)
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[PharmGKB:Curated No association with cardiovascular disease, breast cancer, or lipoprotein levels.]
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[PharmGKB:Curated Associated with femoral BMD in men and left ventricular mass and left ventricular wall thickness in women.]
References:1
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rs1076991 C > T exerts a significant effect on promoter activity in vitro and along with rs2236225 G > A influences embryonic development. Common genetic polymorphisms affect the human requirement for the nutrient choline. Neural tube defects and folate pathway genes: family-based association tests of gene-gene and gene-environment interactions. Gene response elements, genetic polymorphisms and epigenetics influence the human dietary requirement for choline. Lymphocyte gene expression in subjects fed a low-choline diet differs between those who develop organ dysfunction and those who do not. Folate and one-carbon metabolism gene polymorphisms and their associations with oral facial clefts. Association of polymorphisms in one-carbon metabolizing genes and lung cancer risk: a case-cont...
Frequency: 27.4%
References:1
References:1
Frequency: 15.2%
References:4
References:4
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Identification of DIO2 as a new susceptibility locus for symptomatic osteoarthritis. A common variation in deiodinase 1 gene DIO1 is associated with the relative levels of free thyroxine and triiodothyronine. Cellular and molecular basis of deiodinase-regulated thyroid hormone signaling. The -258A/G (SNP rs12885300) polymorphism of the human type 2 deiodinase gene is associated with a shift in the pattern of secretion of thyroid hormones following a TRH-induced acute rise in TSH.
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[PharmGKB:Curated The -58C allele of the human beta2 bradykinin receptor gene has been associated with hypertension in a Chinese Han population and an African American population.]
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Bladder cancer predisposition: a multigenic approach to DNA-repair and cell-cycle-control genes. Genetic susceptibility to renal cell carcinoma: the role of DNA double-strand break repair pathway. Associations between single nucleotide polymorphisms in double-stranded DNA repair pathway genes and familial breast cancer. Disease-associated mutations that alter the RNA structural ensemble. DNA repair gene and MTHFR gene polymorphisms as prognostic markers in locally advanced adenocarcinoma of the esophagus or stomach treated with cisplatin and 5-fluorouracil-based neoadjuvant chemotherapy.
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rs2494732 is a SNP in the AKT1 gene, encoding one of three serine/threonine-protein kinases regulating numerous processes such as cell survival, growth and angiogenesis. Medical conditions that may be linked to the rarer (minor) rs2494732(C) allele include drug response, schizophrenia, and drug-related psychoses, in particuler, cannabis-related psychosis. A case-control study of 489 first-episode psychosis patients concluded that while rs2494732 was not associated with an increased risk of a psychotic disorder, with lifetime cannabis use, or with frequency of use, there was a significant association between psychosis and cannabis use. rs2494732(C;C) individuals with a history of cannabis use had an increased likelihood of a psychotic disorder (odds ratio 2.18, CI: 1.1 - 4.3) when compared ...
References:1
in ALZ patients, increased risk of delusions
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A significant association between delusions and the rs6494223(T) allele (odds ratio 1.63, CI: 1.22-2.17, p = 0.014, ) was found in a cohort of Alzheimer's disease patients in Northern Ireland.
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[GWAS:Response to haloperidol in psychosis]
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[PharmGKB:Curated Risk or phenotype-associated allele: None. Phenotype: Variants identified in a screen of 13 genes involved in the gemcitabine drug metabolic pathway. For the non-synonymous SLC28A2:283A>C (R75S) SNP, the C (75Ser) allele was at frequency was 0.34 and 0.08 in Europeans and Africans, respectively. There was a significant difference between ethnic groups in genotype frequency distribution (p < 0.001). Study size: 187. Study population/ethnicity: Healthy, unrelated blood donors of European (n = 95) and African (n = 92) descent. Significance metric(s): p < 0.001. Type of association: GN.]
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[GWAS:None]
References:2
carrier of one CYP1A2*1D allele
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rs35694136, also known as -2467delT, is a SNP in the CYP1A2 gene. The rs35694136(-) allele defines the CYP1A2*1D variant.
References:1
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Cholinergic nicotinic receptor genes implicated in a nicotine dependence association study targeting 348 candidate genes with 3713 SNPs. No evidence for association between 19 cholinergic genes and bipolar disorder. The CHRNA5/A3/B4 gene cluster variability as an important determinant of early alcohol and tobacco initiation in young adults. Identification of pharmacogenetic markers in smoking cessation therapy. Variants in nicotinic receptors and risk for nicotine dependence. Genetic variability in nicotinic acetylcholine receptors and nicotine addiction: converging evidence from human and animal research. Nicotinic receptor gene variants influence susceptibility to heavy smoking. Risk for nicotine dependence and lung cancer is conferred by mRNA expression levels and amino acid change in C...
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[OMIM:CHOLINERGIC RECEPTOR, NEURONAL NICOTINIC, ALPHA POLYPEPTIDE 5; CHRNA5]
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[PharmGKB:Curated This SNP is not associated with dichotomy in the severity of early onset nicotine addiction, as assessed by the FTND (Fagerstrom Test of Nicotine Dependence). Haplotype B, which contains this SNP, is also not associated with this phenotype.]
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[PharmGKB:Curated The T allele of this SNP is associated with protection from early onset nicotine addiction, i.e., daily smoking commencing at or before age 16. Haplotype C, which is defined by the T allele of this SNP and the A allele of rs578776, is similarly associated with protection from early onset nicotine dependence.]
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identifies a region associated with nicotine dependence in this particular study (1,050 dependents, 879 non-dependent controls, all of European descent), noted as distinct from the loci which rs16969968 defines Cholinergic nicotinic receptor genes implicated in a nicotine dependence association study targeting 348 candidate genes with 3713 SNPs. Variants in nicotinic receptors and risk for nicotine dependence. Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence. Genetic variability in nicotinic acetylcholine receptors and nicotine addiction: converging evidence from human and animal research. Familial aggregation of common sequence variants on 15q24-25.1 in lung cancer. Association of a single nucleotide polymorphism in neuronal...
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[PharmGKB:Non-Curated altered kinetics of gemcitabine in transfected cells]
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[PharmGKB:Curated Risk or phenotype-associated allele: None. Phenotype: Variants identified in a screen of 13 genes involved in the gemcitabine drug metabolic pathway. For the SLC28A1:1383C>T SNP, the T allele was at frequency was 0.08 and 0.05 in Europeans and Africans, respectively. There was no significant difference between ethnic groups in genotype frequency distribution (p > 0.05). Study size: 185. Study population/ethnicity: Healthy, unrelated blood donors of European (n = 91) and African (n = 94) descent. Significance metric(s): Not significant, p > 0.05. Type of association: GN.]
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[PharmGKB:Curated Risk or phenotype-associated allele: None. Phenotype: Variants identified in a screen of 13 genes involved in the gemcitabine drug metabolic pathway. For the non-synonymous SLC28A1:1576T>C (N521D) SNP, the C (521Asp) allele was at frequency was 0.47 and 0.00 in Europeans and Africans, respectively. There was a significant difference between ethnic groups in genotype frequency distribution (p < 0.001). Study size: 185. Study population/ethnicity: Healthy, unrelated blood donors of European (n = 94) and African (n = 91) descent. Significance metric(s): p < 0.001. Type of association: GN.]
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Genetic polymorphisms in the nucleotide excision repair pathway and lung cancer risk: a meta-analysis. Polymorphisms in DNA repair genes, smoking, and bladder cancer risk: findings from the international consortium of bladder cancer.
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[PharmGKB:Curated SNP is associated with the onset of toxicity to methotrexate in patients with psoriasis.]
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[PharmGKB:Curated SNP influences the efficacy of methotrexate in patients with psoriasis.]
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The ABCC6 rs2238472 G variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.006 Type of association: CO; TOX] [OMIM:PSEUDOXANTHOMA ELASTICUM]
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[GWAS:Response to irinotecan and platinum-based chemotherapy in non-small-cell lung cancer]
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[PharmGKB:Curated This variant in the SCNN1B gene showed the most significant association with fluid retention/oedema in participants diagnosed with T2DM receiving farglitazar plus insulin or glyburide combination therapies. But this association has low penetrance in the fluid retention/oedema case population reflecting that SCNN1B variation may be only one of the covariates that contribute to the development of PPAR[gamma]-induced fluid retention.]
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[PharmGKB:In-Depth This promoter region SNP is tightly linked to the *2 variant and may be responsible for some of the functional effects that have been attributed to *2. It has been associated with decreased platelet SULT1A1 activity in African-Americans and increased activity in Caucasians.]
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[PharmGKB:In-Depth This promoter region SNP is tightly linked to the *2 variant and may be responsible for functional effects that have been attributed to *2.]
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rs1801030 (Met223Val) is a snp within SULT1A1 (Sulfotransferase 1A1) and defines the SULT1A1*3 allele. [PharmGKB:In-Depth SULT1A1*3 is the second most common SULT1A1 SNP.]
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[PharmGKB:In-Depth May be associated with a higher warfarin dose phenotype]
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[PharmGKB:Curated This SNP is the tagging SNP for VKORC1*2.]
References:7
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[PharmGKB:Curated This SNP is the tagging SNP for VKORC1*4.]
References:4
References:1
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associations with higher warfarin dose, namely, VKORC1-8191 (rs61162043, P = 0.0041) and 18786 in CYP2C9 (rs7089580, P = 0.035) independent of the previous associations with these genes
may be associated with ADHD
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T allele may be associated with Attention deficit hyperactivity disorder.
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[GWAS:Response to dabigatran etexilate treatment]
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A allele associated with better response to treatment of ADHD with atomoxetine.
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Cholesterol ester transfer protein, interleukin-8, peroxisome proliferator activator receptor alpha, and Toll-like receptor 4 genetic variations and risk of incident nonfatal myocardial infarction and ischemic stroke. Cholesteryl ester transfer protein (CETP) genetic variation and early onset of non-fatal myocardial infarction. Genetic-epidemiological evidence on genes associated with HDL cholesterol levels: a systematic in-depth review.
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Physiogenomic analysis of weight loss induced by dietary carbohydrate restriction. Physiogenomic comparison of human fat loss in response to diets restrictive of carbohydrate or fat. Genetic-epidemiological evidence on genes associated with HDL cholesterol levels: a systematic in-depth review. TagSNP transferability and relative loss of variability prediction from HapMap to an admixed population. Analysis of recently identified dyslipidemia alleles reveals two loci that contribute to risk for carotid artery disease. Polymorphism in the CETP gene region, HDL cholesterol, and risk of future myocardial infarction: Genomewide analysis among 18 245 initially healthy women from the Women's Genome Health Study. Genetics and beyond--the transcriptome of human monocytes and disease susceptibility. ...
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The frequency of remission from rheumatoid arthritis upon leflunomide treatment was increased in rs3213422(C) allele carriers compared with patients with the A allele in a study of 147 patients. [PharmGKB:Curated This variant is associated with leflunomide treatment outcome in a study consisting of 147 patients with rheumatoid arthritis. The C allele carriers tend to have increased frequency of remission compared with patients with the A allele.]
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[PharmGKB:Curated This variant is associated with end-of-induction minimal risidual disease (MRD) in childhood acute lymphoblastic leukemia (ALL) from 2 independent cohorts (GWAS result). Risk Allele: G, MAF= 0.44, combined P value= 2.08E-04. It is also associated with greater methotrexate clearance.]
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[PharmGKB:Non-Curated Haplotypes containing the variant showed decreased luciferase activity in reporter assays in cells and in vivo assay.]
References:1
normal
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rs1042173 is a SNP in the solute carrier family 6 (neurotransmitter transporter, serotonin), member 4 SLC6A4 gene. A study of 275 patients seeking treatment for alcoholism concluded that Caucasians of with the rs1042173(T;T) genotype consumed an average of 11.17 drinks per drinking day, compared with an average of 8.58 for carriers of a rs1042173(G) allele (p = 0.0034). While this held true for both men and women, this association was not seen in Hispanics.
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MCP-1 gene haplotype association in biopsy proven giant cell arteritis. Polymorphisms in the genes encoding chemokine receptor 5, interleukin-10, and monocyte chemoattractant protein 1 contribute to cytomegalovirus reactivation and disease after allogeneic stem cell transplantation. Monocyte chemotactic protein-1 single nucleotide polymorphisms do not confer susceptibility for the development of adult onset polymyositis/dermatomyositis in UK Caucasians. Association of the -2510A/G chemokine (C-C motif) ligand 2 polymorphism with knee osteoarthritis in a Korean population. Comprehensive analysis of the candidate genes CCL2, CCR2, and TLR4 in age-related macular degeneration. Polymorphisms affecting gene transcription and mRNA processing in pharmacogenetic candidate genes: detection through ...
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23andMe blog Influences QT interval DNA repair and cell cycle control genes and the risk of young-onset lung cancer. Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival. Genetic variation in immune regulation and DNA repair pathways and stomach cancer in China.
References:2
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rs4796793, a SNP in the 5' region of the signal transducer and activator 3 STAT3 gene, has been linked in a study of 75 Japanese patients to (successful) response to interferon-alpha immunotherapy for metastatic kidney cancer. From this paper : '... rs4796793 was the most significant predictor of IFN-alpha response (odds ratio [OR] = 2.73; 95% CI, 1.38 to 5.78). The highest OR was shown in the (C;C) genotype ... compared to the (G;G) + (G;C) genotypes (OR = 8.38, 95% CI, 1.63 to 42.96).' [PharmGKB:Curated Risk or phenotype-associated allele: C Phenotype: Metastatic renal cell carcinoma patients with the CC genotype of STAT3 rs4796793 were more likely to respond to interferon alpha therapy than those with the GC or GG genotype. Study size: 75 (29 responders and 46 non-responders). Study po...
Frequency: 49.6%
References:2
References:2
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23andMe blog blood pressure Confirmation of top polymorphisms in hypertension genome wide association study among Han Chinese. Pharmacogenetic implications for eight common blood pressure-associated single-nucleotide polymorphisms. [GWAS:Diastolic Blood Pressure]
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[PharmGKB:Curated Risk or phenotype-associated allele: GG. Phenotype:Increased risk of diabetes associated with thiazide use, this risk was more increased for ACE GG subjects Study size: 497 incident cases of type 2 diabetes and 2,633 controls. metric(s): SI 1.70 (95% CI: 1.08-2.66). Type of association: GN.]
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A and G alleles of rs4343 are strongly associated marking insertion and deletion alleles of ACE I/D respectively. For those looking for the ACE Alu Insertion/Deletion, this is a very good substitute for people searching for ACE Del16. G would mean deletion. A haplotype of rs4311, rs4343, rs699 increases risk of diabetic nephropathy 4x. [PharmGKB:Curated While the ACE:I/D has dbSNP identifiers rs1799752, rs4340, rs13447447 and rs4646994, measurement of a single base at these positions does not give an informative genotype. In Europeans, rs4343 is in complete LD with the ACE:I/D, with the A and G alleles of rs4343 marking the insertion and deletion alleles of ACE:I/D respectively.] [GWAS:Angiotensin-converting enzyme activity]
slower responder
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This SNP in the ACE gene, also known as G12269A, is reported to influence how quickly African Americans respond to the anti-hypertensive drug ramipril. rs4344(A;A) and rs4344(G;G) homozygotes are able to reach lower blood pressure levels upon treatment with ramipril sooner than rs4344(A;G) heterozygotes. The odds ratio reported for this study, comparing both homozygotes to heterozygotes, is 1.86 (CI: 1.32-3.23). Note that this SNP is in almost complete linkage disequilibrium with the insertion/deletion ACE gene SNP.
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[GWAS:Response to methotrexate in rheumatoid arthritis]
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[PharmGKB:Curated In a Chinese population, this SNP was significantly associated with blood pressure response to nifedipine treatment.]
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rs2569190, also known as C260T, is a SNP in the CD14 gene. rs2569190(C) (frequency = 39%) increased stroke risk among smokers (OR = 2.05, 95% CI=1.09-3.86, p=0.03), but not among non-smokers (OR = 0.93, 95% CI=0.62-1.39, p=0.72) rs1295685 and rs20541 were significantly associated with elevated IgE levels in pooled analyses. rs2569190(T;T) and rs2569191(C;C) genotypes associated with lower IgE A meta-analysis of 7 studies (comprising a total of 1488 patients and 1600 control subjects) found no significant association between rs2569190 and cerebrovascular diseases.
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Polymorphisms in inflammation-related genes are associated with susceptibility to major depression and antidepressant response. A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data. [PharmGKB:Curated This variant is associated with response to escitalopram and nortriptyline in a study of 760 adult patients with moderate-to-severe depression.]
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A US study of 1,172 lymphoma patients and 982 controls looked at 57 SNPs in 36 immune function genes. Five SNPs in two cytokine genes, tumor necrosis factor-alpha and lymphotoxin-alpha, were associated with a 1.31x increase in non-Hodgkin lymphoma (OR, 1.31; 95% CI, 1.06-1.63; P = 0.01) and with a 1.64x increase in the subtype known as diffuse large B cell lymphoma (OR, 1.64; 95% CI, 1.23-2.19; P = 0.0007). The other four SNPS are listed below. The cytokine genes affect inflammatory and innate immune responses. * rs1800629 * rs361525 * rs1799724 * rs2239704 [PharmGKB:Curated Risk or phenotype-associated allele, tested allele: unspecified; minor allele designation varies by ethnicity in dbSNP Phenotype: In 114 cases and 414 controls (n = 528), univariate analysis of disease association sho...
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827 males and 709 females, 606 subjects without cancer and 930 subjects with various cancers *rs1041981(A;C) (C804A, T60N) associated with lung cancer (CA + AA: CC, adjusted OR = 0.60, 95% CI = 0.37 - 0.97), in males but not in females [OMIM:MYOCARDIAL INFARCTION, SUSCEPTIBILITY TO]
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[PharmGKB:Curated The G allele of this SNP is part of a haplotype that has been associated with protection from hypersensitivity to carbamazepine.]
1.5x risk of Crohn's disease
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rs1000113 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with heterozygotes is 1.54 (CI 1.31-1.82), and for homozygotes, 1.92 (CI 0.92-4.00). [PharmGKB:Non-Curated GWAS Results: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Initial Sample Size: 1,748 cases, 2,938 controls; Replication Sample Size: (see Parkes 2007); Risk Allele: rs1000113-T). This variant is associated with crohn's disease.] [GWAS:Crohn's disease]
Normal risk of developing heart disease
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Affects heart disease risk for both men and women, based on a study of two Finnish population cohorts (HR = 1.31 (1.08-1.60) for CVD, uncorrected p = 0.006 multiplicative model). A meta-analysis of publications through July 2009, totaling 4,386 cases (vs 40,089 controls) concluded that apart from a very weak association with myocardial infarction for the rs1801020 (T;T) + (C;T) compared with (C;C) genotype, (odds ratio 1.13, CI: 1.00 - 1.27), the evidence for an association between F12 -4C>T and venous thromboembolism and myocardial infarction was weak. [OMIM:COAGULATION FACTOR XII; F12]
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[PharmGKB:Curated Risk or phenotype-associated allele: C. Phenotype: A-444C was associated with aspirin-induced urticaria (AIU). The C allele was more frequent in patients with the cutaneous pattern of AIU and in patients with low skin reactivity to histamine. Study size: 110 patients with AIU and 165 nonallergic controls .]
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Polymorphisms in the vascular endothelial growth factor gene and breast cancer in the Cancer Prevention Study II cohort. Large-scale evaluation of candidate genes identifies associations between VEGF polymorphisms and bladder cancer risk. Vascular endothelial growth factor (VEGF) gene (VEGFA) polymorphism can predict the prognosis in acute myeloid leukaemia patients. VEGF polymorphisms and survival in early-stage non-small-cell lung cancer. Vascular endothelial growth factor gene polymorphisms in age-related macular degeneration. Polymorphisms in the vascular endothelial growth factor gene and the risk of familial endometriosis. Genetic polymorphisms of VEGF, interactions with cigarette smoking exposure and esophageal adenocarcinoma risk. Functional genetic polymorphisms and female reprodu...
References:5
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VEGF polymorphisms are associated with severity of diabetic retinopathy. Genetics of VEGF serum variation in human isolated populations of cilento: importance of VEGF polymorphisms.
normal
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This position is referred to as the -1154 position in many VEGF-associated publications. The normal (or wild type) form of this SNP is a (G). The (A) form reduces the activity of this gene, resulting in less VEGF protein. Individuals with one or more rs1570360(A) alleles are reported to be at about a 3 fold higher risk of developing Sudden Infant Death Syndrome . A functional variant of vascular endothelial growth factor is associated with severe ischemic complications in giant cell arteritis. Analysis of vascular endothelial growth factor (VEGF) functional variants in rheumatoid arthritis. Association between functional haplotypes of vascular endothelial growth factor and renal complications in Henoch-Schonlein purpura. Polymorphisms in the vascular endothelial growth factor gene and brea...
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Identification of genes and haplotypes that predict rheumatoid arthritis using random forests. Polymorphisms in the VEGF-A in polypoidal choroidal vasculopathy in a Korean population.
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may be associated with clozapine response in treatment-resistant schizophrenic patients [PharmGKB:Curated Patients with diplotype ACCCTC/GTTGCC, genotypes T/T+T/C, or allele T of marker rs742105 showed a better response to clozapine (0.005</=P</=0.049) in a study of patients with refractory schizophrenia.]
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intelligence related [PharmGKB:Curated Several studies showed an associaction of this SNP in DTNBP1 with schizophrenia and other psychotic disorders, including substance-induced psychosis]
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[OMIM:DYSTROBREVIN-BINDING PROTEIN 1; DTNBP1]
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may be associated with haloperidol response in treatment-resistant schizophrenic patients [PharmGKB:Curated Patients with diplotype ACCCTC/GCCGCC, genotype A/G, or allele A of marker rs909706 have better response to haloperidol (0.007</=P</=0.080) in a study of patients with refractory schizophrenia.]
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Risk alleles for multiple sclerosis identified by a genomewide study. [GWAS:None]
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[PharmGKB:Curated Risk or phenotype-associated allele: C allele. Phenotype: The C allele of rs750332 shows strong association with carbamazepine (CBZ)-induced Stevens-Johnson syndrome (SJS)/Toxic Epidermal Necrolysis (TEN, Lyell's syndrome). Study size: 204. Study population/ethnicity: 60 CBZ-induced SJS/TEN cases and 144 CBZ-tolerant controls of Chinese descent. Significance metric(s): p = 3.04x10(-14), Pc = 8.45x10(-12), OR = 6.41. Type of association: GN; PD; TOX; ADR.]
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23andMe blog psoriasis Europeans *rs610604(G) 1.19x risk [PharmGKB:Non-Curated GWAS results: Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways. (Initial Sample Size: 1,359 cases, 1,400 controls; Replication Sample Size: 5,048 cases, 5,041 controls); (Region: 6q23.3; Reported Gene(s): TNFAIP3; Risk Allele: rs610604-G); (p-value= 0.000000000009).This variant is associated with Psoriasis.] [GWAS:Psoriasis]
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[GWAS:Hepatocellular carcinoma]
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[PharmGKB:Curated Risk or phenotype-associated allele: A allele. Phenotype: The A allele rs2894342, which lies in the promoter of MLN, is associated with carbamazepine (CBZ)-induced maculopapular exanthema (MPE)/ hypersensitivity syndrome (HSS). Study size: 175. Study population/ethnicity: 31 CBZ-induced MPE/HSS cases and 144 CBZ-tolerant controls of Chinese descent. Significance metric(s): p = 0.00342, OR = 2.88. Type of association: GN; PD; TOX; ADR.]
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The PPAR delta SNP rs7769719 A>G was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0055 Type of association: PD; CO]
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rs9296158 rs3800373 rs1360780 rs9470080 linked with the severity of child abuse to predict level of adult PTSD symptoms after correcting for multiple testing. [PharmGKB:Curated This variant is associated with higher chance of response to anti-depressant drugs.]
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The PPAR delta SNP rs6922548 A>G was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0011 Type of association: PD; CO]
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rs20455, often called Arg719 or 719Arg, is a reasonably well studied SNP in the KIF6 gene. The risk allele (encoding the arginine at position 719) is rs20455(C). An extensive 2010 meta-analysis, including over 17,000 patients, suggests this variant does not significantly influence coronary artery disease risk. This SNP is one of the 5 used by Celera's genetic risk score (GRS) for coronary heart disease (CHD). *rs20455, in the KIF6 gene *rs3900940, in the MYH15 gene *rs7439293, in the PALLD gene *rs2298566, in the SNX19 gene *rs1010, in the VAMP8 gene For each of the five variants, the GRS was increased by 1 if the subject was homozygous for the risk variant, unchanged if heterozygous, and decreased by 1 if the individual did not carry the variant. Therefore, individuals carrying all 10 pos...
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[GWAS:Response to irinotecan and platinum-based chemotherapy in non-small-cell lung cancer]
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[PharmGKB:Curated This variant in the corticotropin-releasing hormone receptor-2 gene was associated with acute bronchodilator response in the 608-participant Childhood Asthma Management Program (CAMP), but was not found to be associated in the 427-participant Sepracor study or the 152-participant LODO trial. The mean ages of the participants in the CAMP, Sepracor, and Lodo cohorts were 8.9, 32.6, and 42.9 years of age, respectively. Only Caucasians were analyzed in each of these studies.]
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[PharmGKB:Curated This variant in the corticotropin-releasing hormone receptor-2 gene was associated with acute bronchodilator response in the 427-participant Sepracor study, but not in the 608-participant Childhood Asthma Management Program (CAMP) or the 152-participant LODO trial. The mean ages of the participants in the CAMP, Sepracor, and Lodo cohorts were 8.9, 32.6, and 42.9 years of age, respectively. Only Caucasians were analyzed in each of these studies.]
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ARG1 is a novel bronchodilator response gene: screening and replication in four asthma cohorts. [PharmGKB:Curated Risk or phenotype-associated allele: T Phenotype: The T variant of CRHR2 rs7793837 was associated with reduced acute bronchodilation response to short-acting beta2-agonist treatment in the CAMP and LODO studies but not the Sepracor study. Study size: 607 (CAMP); 152 (LODO); 427 (Sepracor) Study population/ethnicity: Caucasian children with asthma with a mean age of 8.83 years enrolled in the Childhood Asthma Management Program (CAMP); Adult Caucasian participants with asthma enrolled in the Clinical Trial of Low-Dose Theophylline and Montelukast conducted by the American Lung Association Asthma Clinical Research Centers (LODO); Adult Caucasian participants with asthma enrolled...
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[PharmGKB:Curated In a study of ovarian cancer patients (n=104) receiving a cisplatin-cyclophosphamide regimen, the T/T genotype of GSTA1:(-69)C>T polymorphism was associated with increased overall survival.]
References:1
Frequency: 61.9%
References:5
References:5
References:6
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[OMIM:?] [GWAS:Systemic lupus erythematosus]
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[PharmGKB:Curated Risk or phenotype-associated allele: G. Phenotype: The variant 146GG genotype was associated with increased exposure to doxorubicin and its active metabolite doxorubicinol. Study size: 62. Study population/ethnicity: Patients with Breast Neoplasms receiving adjuvant doxorubicin; Asian; Singapore. Type of association: PK.]
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[GWAS:Asthma (childhood onset)]
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[PharmGKB:Curated A study in 243 children with ADHD and their parents suggests a role for the promoter region of the SLC6A3 gene in ADHD susceptibility. In the DSM-IV combined subtype, results showed a preferential transmission of the haplotype A/C/C/C/A derived from five SNPs (rs2550948, rs11564750, rs261759, rs2652511, rs2975223) in 5' region of the SLC6A3 gene.]
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No association of single nucleotide polymorphisms in one-carbon metabolism genes with prostate cancer risk. Lack of association of polymorphisms in homocysteine metabolism genes with pseudoexfoliation syndrome and glaucoma.
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pancreatic cancer 702 cases and 785 controls *rs162049 P = .0018; OR, 1.33; 95% CI: 1.11-1.60 *rs10380 (His595Tyr) P = .0063; OR, 1.45; 95% CI: 1.11-1.88
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[PharmGKB:Curated This variant is a noncoding SNP within 5' UTR of ADRB2, in amino acid residue 19 of the 19 amino acid beta upstream peptide (BUP) affecting ADRB2 expression at the translational level. Arg-19 allele was associated with lower receptor expression.]
complex; see details for increased risks
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Several susceptibilities have been linked to rs1042714, a SNP in the ADRB2 gene that is also known as the Q27E SNP. The rs1042714(C) allele encodes the glutamine (Gln; 'Q'), and the rs1042714(G) allele encodes the glutamic acid (Glu; 'E'). A study of 304 patients found that the Glu27 allele led to increased risk for idiopathic venous thromboembolism; the reported odds ratio was 1.40 (CI: 1.09-1.79, p=0.006) for carriers of at least one risk allele. A study of 334 families with at least one child with autism found that increased risk associated with the rs1042714(G;G) homozygous genotype; the odds ratio reported was between 1.33-1.60 (CI: 1.07-2.58). The risk was approximately doubled among mothers who had clinical markers for pregnancy related stress. In a study of 342 patients with type-2...
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prostate cancer rs3212649 (OR=1.67 (1.07-2.6), P=0.0009) and rs1126643 (OR=1.52 (1.01-2.28), P=0.0088).
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Association study between the serotonin 1A receptor (HTR1A) gene and neuroticism, major depression, and anxiety disorders. SSRI response in depression may be influenced by SNPs in HTR1B and HTR1A. Pharmacogenetics of antidepressant response. Sertraline (Zoloft) response in major depressive disorder is not associated with three 5-HT1A receptor gene polymorphisms (rs6295, rs10042486, or rs1364043) in Chinese-Han patients. [PharmGKB:Curated A study, investigating the response of SSRI in 137 Japanese major depression subjects, observed a significant association of better response to antidepressant in rs10042486 (P < 0.0001), rs6295 (P < 0.0001) and rs1364043 (P = 0.018) genotype carriers (minor allele homozygotes), independently from clinical variables. The rs6295 variant has been found...
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[PharmGKB:Curated Risk or phenotype-associated allele(s): G/G. Phenotype: This SNP was strongly associated with response to treatment, in which 20 subjects with the GG genotype showed minimal changes in panic attack frequency with a relative risk of no response of 4.73. Study size: 102. Study population/ethnicity: patients with a diagnosis of panic disorder receiving sertraline or paroxetine.]
Frequency: 26.1%
References:7
References:7
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[PharmGKB:Curated A study, investigating the response of SSRI in 137 Japanese major depression subjects, observed a significant association of better response to antidepressant in rs10042486 (P < 0.0001), rs6295 (P < 0.0001) and rs1364043 (P = 0.018) genotype carriers (minor allele homozygotes), independently from clinical variables. The rs6295 variant has been found to affect the expression and function of HTR1A. rs6295 is in strong linkage disequilibrium with other polymorphisms of HTR1A.]
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Genetic variation in 3-hydroxy-3-methylglutaryl CoA reductase modifies the chemopreventive activity of statins for colorectal cancer by Lipkin SM, Chao EC, Moreno V, Rozek LS, Rennert H, Pinchev M, Dizon D, Rennert G, Kopelovich L, Gruber SB in Cancer Prev Res (Phila Pa). 2010 May;3(5):597-603. The above study shows that genotyping for HMGCR rs1265464 may help identify the subset of individuals who are most likely to achieve a CRC risk reduction and cholesterol lowering with statins. Compared with individuals not taking statins, the unadjusted odds ratio of colorectal cancer among rs12654264(A;A) statin users was 0.3 (CI: 0.18-0.51) and among rs12654264(T;T) statin users, 0.66 (CI: 0.41-1.06, p-interaction 0.0012). Their data may advance the development of personalized statin use for reduc...
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news three SNPs that appear to have different effects in men and women rs3846662 rs2304130 rs2083637 journal LDL-Cholesterol minor allele was associated with up to 2.2-fold lower expression Common SNPs in HMGCR in micronesians and whites associated with LDL-cholesterol levels affect alternative splicing of exon13. The HMG-CoA reductase gene and lipid and lipoprotein levels: the multi-ethnic study of atherosclerosis. Genetic loci associated with plasma concentration of low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, triglycerides, apolipoprotein A1, and Apolipoprotein B among 6382 white women in genome-wide analysis with replication. Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip. Analysis of recently identifie...
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[GWAS:None]
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prostate cancer treatment response rs2279115 and rs7121 Complex haplotype structure of the human GNAS gene identifies a recombination hotspot centred on a single nucleotide polymorphism widely used in association studies. Polymorphism in maternal LRP8 gene is associated with fetal growth. Differential allelic expression in the human genome: a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression. PTHR1 mutations associated with Ollier disease result in receptor loss of function. Functional genetic polymorphisms and female reproductive disorders: Part I: Polycystic ovary syndrome and ovarian response. A sensitive functional assay reveals frequent loss of genomic imprinting in human placenta. Association of the GNAS locus with severe malaria. Dev...
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associated with vulnerability to nicotine addiction in men. g2b2mh blog rs1044396 mediates effects of nicotine self-medication via parietal cortex. subjects with the (T;T) genotype showed robust brain activity in the parietal cortex while subjects with the (C;C) genotype showed very little change in activity. [PharmGKB:Curated This variant is closely linked to rs2236196 and has been associated with the intensification of nicotine dependence.] [OMIM:CHOLINERGIC RECEPTOR, NEURONAL NICOTINIC, ALPHA POLYPEPTIDE 4; CHRNA4]
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The rs2832407(C) allele has inconsistently been linked to alcoholism and its treatment. Nonetheless, a 2014 report based on 138 patients concludes that rs2832407(C;C) individuals show a greater decrease than non-carriers (of a rs2832407(C) allele) in the number of heavy drinking days per week when taking topiramate at a dose of 200 mg/daily. A follow-up study done 3 and 6 months after treatment seemed to mostly confirm the topiramate benefit preferentially to rs2832407(C;C) individuals.
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[PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: CBR3 11G>A variant was associated with lower doxorubicinol AUC, lower CBR3 expression in breast tumor tissue, greater tumor reduction, and greater percentage reduction of leukocyte and platelet counts at nadir. Study size: 101 Study population/ethnicity: Asian; patients with Breast Neoplasms; Chinese; Malay; Indian Significance metric(s): p = 0.009 (AUC); p = 0.001 (expression); p = 0.015 (tumor reduction); p = 0.03 (leukocyte and platelet counts). Type of association: PK; TOX]
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Epistatic interaction of CREB1 and KCNJ6 on rumination and negative emotionality. Effect sizes in experimental pain produced by gender, genetic variants and sensitization procedures. [PharmGKB:Curated Risk or phenotype-associated genotype: AA. Phenotype: The average methadone dose during the first year of substitution therapy were significantly larger in AA carriers (n=4) than in the other rs2070995 genotypes (p=0.003). Study Size: 85. Study population: Caucasian.]
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[GWAS:None]
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[GWAS:None]
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common trait being optimism [GWAS:Common traits (Other)]
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[PharmGKB:Curated Risk or phenotype-associated allele: heterozygote CT bears the greatest genotypic risk. Phenotype: A significant difference in 3-month progression-free survival was associated with the rs1051298 genotype (CC vs. CT vs. TT: 57%, 29%, 78%) (p = 0.01); and median progression-free survival was associated with the rs1051298 genotype (CC vs. CT vs. TT: 5.7, 2.8, 4.7 months) (p = 0.05). Study size: from a study using 48 patients with metastatic or stage IIIB nonsquamous non-small-cell lung cancer patients given combined pemetrexed/bevacizumab treatment. Significance metric(s): p = 0.01, p = 0.05. Type of association: CO, GN]
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This is one of the SNPs reported by NutraHacker.
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[PharmGKB:Curated This promoter variant is associated with breast cancer risk reduction in two of three case control studies. Functional studies showed that it altered nuclear protein binding patterns and was associated with the up-regulation of transcription, possibly resulting in increased COMT activity.]
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part of a three marker haplotype rs737865-rs4680-rs165599 COMT haplotypes at rs737865 and rs165599 may predict a favorable outcome for bupropion treatment for smoking cessation. We have typed the IVS 1 rs737865 and 3' rs615599 sites and also included a novel IVS 1 indel polymorphism. We report that the schizophrenia-associated haplotype is significantly heterogeneous in populations worldwide. may affect non-Hodgkin lymphoma, anxiety-related personality traits Also mentioned in these PMIDs * * * * * * [PharmGKB:Curated This variant may predict a favorable outcome for bupropion treatment for smoking cessation] [OMIM:CATECHOL-O-METHYLTRANSFERASE; COMT]
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower COMT enzymatic activity, therefore higher dopamine levels; lower pain threshold, enhanced vulnerability to stress, yet also more efficient at processing information under most conditions *rs4680(G) = Warrior. Val, less exploratory, higher COMT enzymatic activity, therefore lower dopamine levels; higher pain threshold, better stress resiliency, albeit with a modest reduction in executive cognition performance under most conditions Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis; summary at ) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compar...
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[PharmGKB:Curated On the basis of subjects' pain responsiveness, haplotypes involving rs6269 (A/G), rs4633 (C/T), rs4818 (C/G), and rs4680 (G/A) were designated as low (low pain sensitivity (LPS) haplotype; GCGG), average (average pain sensitivity (APS) haplotype; ATCA), or high (high pain sensitivity (HPS) haplotype; ACCG) pain sensitive.]
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anxiety-related personality traits, ADHD, schizophrenia part of a three marker haplotype rs737865-rs4680-rs165599 epistasis between SNPs in COMT (rs2097603, Val158Met (rs4680), rs165599) and polymorphisms in other schizophrenia susceptibility genes popular in pubmed is associated with bipolar disorder and influences prefrontal aspects of verbal memory in bipolar patients and healthy controls. [PharmGKB:Curated In a study of 78 African American and 65 white patients diagnosed with schizophrenia or schizoaffective disorder, this SNP in the COMT gene was found to have significant associations with response to risperidone over 2-12 weeks in both African-American and white patients.] [OMIM:CATECHOL-O-METHYLTRANSFERASE; COMT]
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Seems to play a role in the brain This is a synonymous change. it does not affect the amino acid. [PharmGKB:Curated On the basis of subjects' pain responsiveness, haplotypes involving rs6269 (A/G), rs4633 (C/T), rs4818 (C/G), and rs4680 (G/A) were designated as low (low pain sensitivity (LPS) haplotype; GCGG), average (average pain sensitivity (APS) haplotype; ATCA), or high (high pain sensitivity (HPS) haplotype; ACCG) pain sensitive.] [OMIM:CATECHOL-O-METHYLTRANSFERASE; COMT]
normal risk
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rs140504, a SNP in the BCR gene on chromosome 22, has been associated with increased risk for bipolar disorder. The odds ratio for carriers of the minor allele (G) are reported as 1.45 (CI:1.11 - 1.84, p=0.0054) based on a study of 171 Japanese patients. [OMIM:MAJOR AFFECTIVE DISORDER 1; MAFD1]
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[PharmGKB:Curated Risk or phenotype-associated allele: rs2267076 T allele Phenotype: Carriers of 1 or 2 copies of the T allele for rs2267076 showed increased risk of any (OR = 2.1, CI 1.05-4.27, p = 0.02) or gastrointestinal-specific (OR = 1.77, CI = 0.65-5.77, p = 0.22) adverse events. Study size: 309 RA patients, including 147 good MTX responders, 101 MTX inefficacy failures, and 61 adverse event (AE) MTX failures (e.g. gastrointestinal (n = 24), abnormal liver function tests (n = 20), haematological (n = 7), skin rashes (n = 6), and other (n = 17). Study population/ethnicity: Rheumatoid arthritis (RA) patients aged over 18 yrs, of White Caucasian ethnic origin, classified as having RA according to ARA criteria that were retrospectively recruited from University Hospital of North Staffor...
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[PharmGKB:Curated Risk or phenotype-associated allele: rs5760410 G allele. Phenotype: Carriers of 1 or 2 copies of the G allele for rs5760410 showed increased risk of any (OR = 3.07, CI 1.22-8.76, p = 0.01) or gastrointestinal-specific (OR = 4.58, CI = 1.01-42.05, p = 0.03) adverse events. Study size: 309 RA patients, including 147 good MTX responders, 101 MTX inefficacy failures, and 61 adverse event (AE) MTX failures (e.g. gastrointestinal (n = 24), abnormal liver function tests (n = 20), haematological (n = 7), skin rashes (n = 6), and other (n = 17). Study population/ethnicity: Rheumatoid arthritis (RA) patients aged over 18 yrs, of White Caucasian ethnic origin, classified as having RA according to ARA criteria that were retrospectively recruited from University Hospital of North Staf...
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rs1007888(C;C) was associated with an increased risk of type-2 diabetes in women [hazard ratio (95% CI) 1.74 (1.02-2.97)], but not in men [1.17 (0.75-1.81)]. Macrophage migration inhibitory factor in acute lung injury: expression, biomarker, and associations. Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes. The macrophage migration inhibitory factor (MIF) gene polymorphism in Czech and Russian patients with myocardial infarction. Macrophage migration inhibitory factor: critical role in obesity, insulin resistance, and associated comorbidities. Usefulness of Mendelian randomization in observational epidemiology.
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[PharmGKB:Curated Risk or phenotype-associated allele: rs3761422 T allele. Phenotype: Carriers of 1 or 2 copies of the T allele for rs3761422 showed increased risk of any (OR = 2.11, CI = 1.04-4.39, p = 0.02) or gastrointestinal-specific (OR = 1.91, CI = 0.69-5.77, p = 0.17) adverse events. Study size: 309 RA patients, including 147 good MTX responders, 101 MTX inefficacy failures, and 61 adverse event (AE) MTX failures (e.g. gastrointestinal (n = 24), abnormal liver function tests (n = 20), haematological (n = 7), skin rashes (n = 6), and other (n = 17). Study population/ethnicity: Rheumatoid arthritis (RA) patients aged over 18 yrs, of White Caucasian ethnic origin, classified as having RA according to ARA criteria that were retrospectively recruited from University Hospital of North Sta...
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Association between ADORA2A and DRD2 polymorphisms and caffeine-induced anxiety. Adenosine A(2A) receptor gene (ADORA2A) variants may increase autistic symptoms and anxiety in autism spectrum disorder. [PharmGKB:Curated Risk or phenotype-associated allele: rs2236624 T allele. Phenotype: Carriers of 1 or 2 copies of the T allele for rs2236624 showed increased risk of any (OR = 2.73, CI 1.4-5.39, p = 0.002) or gastrointestinal-specific (OR = 2.7, CI = 1.02-7.49, p = 0.04) adverse events. Study size: 309 RA patients, including 147 good MTX responders, 101 MTX inefficacy failures, and 61 adverse event (AE) MTX failures (e.g. gastrointestinal (n = 24), abnormal liver function tests (n = 20), haematological (n = 7), skin rashes (n = 6), and other (n = 17). Study population/ethnicity: Rheumatoid...
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[GWAS:Age-related macular degeneration]
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[PharmGKB:Curated The C allele of this variant is associated with increased response of patients with bipolar disorder to lithium treatment relative to that observed in patients carrying two copies of the T allele. This association was observed in two separate cohorts: one of 188 patients, and one of 151 patients.]
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[PharmGKB:Curated Risk or phenotype-associated allele: AA. Phenotype: Homozygous AA at this SNP was associated with chronic cardiotoxicity in response to doxorubicin. Study size: 1697. Study population/ethnicity: Participants of the German non-Hodgkin lymphoma study. Significance metric(s): OR = 2.5; 95% CI, 1.3 to 5.0. Type of association: PD; ADR; TOX.]
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[PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: This SNP was associated with acute cardiotoxicity in response to doxorubicin. Study size: 1697. Study population/ethnicity: Participants of the German non-Hodgkin lymphoma study. Significance metric(s): OR = 2.6; 95% CI, 1.3 to 5.1. Type of association: PD; ADR; TOX.]
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[PharmGKB:Curated This variant is in intron 3 of PICK1 and has been significantly associated with methamphetamine abusers in general, and associated with those with spontaneous relapse of psychosis.]
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[PharmGKB:Curated This variant is in intron 4 of PICK1 and has been significantly associated with methamphetamine abusers with spontaneous relapse of psychosis.]
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This SNP, located in the 3' UTR of the CSNK1E gene, has been associated with sensitivity to the acute effects of d-amphetamine. Sensitivity to psychoactive drugs has been associated with potential to develop drug abuse. The more sensitive allele is rs135745(C). However, in a separate study, this SNP did not affect susceptibility to methamphetamine dependence or psychosis, at least in a Japanese population. Note: orientation relative to dbSNP needs to be confirmed/checked.
References:5
carrier of one CYP2D6*41 allele
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rs28371725, also known as 2988G>A, is a SNP in the CYP2D6 gene. The rs28371725(A) allele defines the CYP2D6*41 variant, which has decreased activity. 23andMe also has SNP i4001476 at the same position. [PharmGKB:In-Depth This variant is part of the CYP2D6*41 IM haplotype. Plasma concentrations of metoprolol were shown to be were 4.9-fold higher in the PMs, with greater reductions in heart rate, diastolic blood pressure, and mean arterial pressure in PMs than in non-PMs.]
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[PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: The AA homozygote was associated with lower clearance of docetaxel. Study size: 31. Study population/ethnicity: Patients with Non-Small-Cell Lung Carcinoma. Significance metric(s): Type of association: PK.]
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rs1414334(C) associated with the metabolic syndrome in patients using *clozapine (OR, 9.20; 95% CI, 1.95-43.45) *risperidone (OR, 5.35; 95% CI, 1.26-22.83) [PharmGKB:Curated Risk or phenotype-associated allele: C. Phenotype: In a replication study, the C allele of HTR2C rs1414334 polymorphism is associated with development of the metabolic syndrome during treatment with antipsychotics. Study size: 186. Study population/ethnicity: 93% Caucasian; European; Dutch; The Netherlands. Significance metric(s): OR = 3.73; 95% CI= 1.29-10.79; P = 0.015. Type of association: CO.]
normal
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rs3813929, also known as -759C/T, is a SNP in the 5-hydroxytryptamine (serotonin) receptor 2C HTR2C gene. A study of 107 patients with schizophrenia being treated with olanzapine reported a protective effect against weight-gain from the (T) allele of this SNP; zero patients (of 28) with a rs3813929(T) allele had a body mass index increase of >=10% (p=0.002), whereas (C;C) homozygotes did. This effect may also involve nearby SNP rs518147. T allele showed borderline significant association with higher BMI and incidence of lifetime major depressive disorder among 4978 persons from the European Prospective Investigation into Cancer (EPIC)-Norfolk study, however, only the association with BMI remained borderline significant within the full EPIC-Norfolk cohort (20,981 persons) The association...
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In 2009, a large, multi-sample replication study failed to find any significant association with Intelligence for this or other SNPs in CHRM2 . Earlier work had observed that this snp (and perhaps its neighbors) influenced intelligence and alcohol dependence CHRM2 gene predisposes to alcohol dependence, drug dependence and affective disorders: results from an extended case-control structured association study. And the earlier and or this pdf poster show association between the CHRM2 gene and intelligence . In this study of ~300 Caucasians, the (T;T) genotype appeared to typically have a 4 point higher IQ than the (A;T) genotype, which had a 4 point higher IQ (on average) than the (A;A) genotype. A nearby SNP, rs324640, showed similar results to rs324650, and was in linkage disequilibrium (...
a common variant
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The wild type (normal) allele at this SNP is (G). The (A) variant indicates the presence of a non-wild type CYP2D6 variant, but it appears in many different variants so it can not be used to determine the presence of any particular variant. Inheriting a normal number of copies of this allele results in CYP2D6 function that is indistinguishable from wild-type (normal) activity. However, this variant has been seen present in higher copy numbers, and in these cases, can result in the ultrafast metabolizer phenotype . [PharmGKB:In-Depth Risk or phenotype-associated allele: T. Phenotype: The CYP2D6*2A haplotype was associated with lower incidence of breast cancer on tamoxifen compared to placebo in a prevention study. The CYP2D6*2A allele may be associated with increased efficacy of tamoxifen....
a common variant
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rs1080985 is a SNP near the CYP2D6 gene. Depending on the publication source, it may be called '-1584C/G' or '1496C>G' or the like. The wild type (normal) allele at this SNP is (C). The (G) variant indicates the presence of a non-wild type CYP2D6 variant, but it appears in many different variants so it can not be used to determine the presence of any particular variant. The rs1080985(G) allele defines the CYP2D6*2A variant, which has been reported to have relatively normal function yet in some cases may also lead to the intermediate metabolism phenotype. Please be careful when interpreting results for this SNP as it is in dbSNP and SNPedia in minus orientation where the risk allele is G, but test results are usually in plus orientation where the risk allele is C. This SNP has an ambiguo...
common
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rs1080983 is a SNP near the 5' end of the CYP2D6 gene. Little is known of the significance of either allele.
common in complete genomics
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[PharmGKB:Non-Curated GWAS Results: Whole genome association study identifies polymorphisms associated with QT prolongation during iloperidone treatment of schizophrenia (Initial Sample Size: 183 individuals; Replication Sample Size: NR; Risk Allele: rs4933824-T). This variant is associated with Response to iloperidone treatment (QT prolongation).] [GWAS:Response to iloperidone treatment (QT prolongation)]
normal
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rs5219, also known as E23K, is a SNP in the KCNJ11 gene. The association between type-1 diabetes and rs5219 is mentioned as being replicated in ; there is also a 90% correlation between rs5219 and rs5215. This SNP is one of 4 relatively common SNPs reported to represent risk for type-2 diabetes in the DESIR prospective study of 3,877 Caucasian participants. Under an additive model, the odds ratio for the minor (risk) allele (T) is 1.15 (CI: 0.95-1.4, p=0.2, ie not significant). But for the 4 SNPs, each risk allele increased type-2 diabetes risk by 1.34x (p=2x10e-6), with an odds ratio of 2.48 (CI: 1.59-3.86) for carriers of 4 or more compared to those with one or none (risk alleles). Genotyping of ~4000 Chinese as well a meta-analysis concluded that rs5219 was associated with type-2 diabet...
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news The effectiveness of 17 alpha-hydroxyprogesterone caproate for prevention of recurrent preterm birth is influenced by SNPs. Black women *rs471767 homozygous for the major allele treatment significantly reduced the rate of preterm birth. *rs578029 who had a least one copy of the major allele, treatment significantly reduced in preterm birth non-black women *a least one copy of the minor allele of rs503362 had a significant reduction with treatment *with at least one copy of the minor allele of rs666553 had a significant reduction in very preterm birth
Magnitude: 0
Frequency: 26.5%
Repute:Good
References:5
Frequency: 26.5%
Repute:Good
References:5
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The rs964184(G;G) genotype is associated with hypertriglyceridemia. [PharmGKB:Non-Curated GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 11q23.3; Reported Gene(s): APOA1, APOC3, APOA4, APOA5; Risk Allele: rs964184-G); (p-value= 0.000000000001).This variant is associated with HDL cholesterol.] [GWAS:HDL cholesterol]
normal
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rs662799 is a SNP in the APOA5 gene. The rarer rs662799(C) allele has been associated in multiple reports (cited below) to be associated with higher triglyceride levels. Independently of triglyceride levels, perhaps, a study based on 1,864 Italian patients <45 years old at the time of their first heart attack (myocardial infarction) concluded that this SNP is associated with higher risk for an early heart attack, with a per C allele odds ratio of 1.44 (CI: 1.23-1.69, p = 6.7 × 10(-5)). This SNP has also been reported to help prevent weight gain from high fat diets. 1,073 men and 1,207 women participating in the Framingham Offspring Study rs662799 -1131T>C in modulates the effect of fat intake on BMI and obesity risk in both men and women. Individuals with at least one C allele g...
normal
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rs3184504 is a nonsynonymous SNP in the SH2B3 gene, and it is also known as R262W. In a recent (2008) study of non-HLA SNP associations of 1600+ celiac disease patients, this SNP was considered one of the most significant. The odds ratio for the minor allele was 1.19 (CI:1.10-1.30, p=1.33x10e-7). rs653178, another SNP in strong linkage disequilibrium (r<sup>2</sup>>0.99) with rs3184504, was also associated with celiac disease. associated with type-1 diabetes 23andMe blog coronary artery disease and heart attack SNP Risk Version Effect *rs646776 T 1.19 *rs17465637 C 1.14 *rs1746048 C 1.17 *rs6725887 C 1.17 *rs11206510 T 1.15 *rs3184504 T 1.13 *rs2306374 C 1.15 *rs3782886 C 1.44 23andMe blog blood pressure Pharmacogenetic implications for eight common blood pressure-associated...
normal risk
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rs7997012, located in an intron of the HTR2A gene, was found to be associated with a somewhat increased rate of successful response to treatment of depression with the drug citalopram. From this article : 'HTR2A encodes the serotonin 2A receptor, which is downregulated by citalopram. Participants who were homozygous for the A allele had an 18% reduction in absolute risk of having no response to treatment, compared with those homozygous for the other allele.' * See also Anxiety Blog posting [PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: Patients with the 5-HTR2A intron 2 (rs7997012) AA genotype suffered from more pronounced side effects compared to carriers of the GA or GG genotype. Study size: 124. Study population/ethnicity: Caucasian; Patients with psychiatric diso...
normal risk for Alzheimer's; higher total and LDL cholesterol in females
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RNA made containing the rs688(T) SNP, a variant near exon 12 of the low-density lipoprotein receptor (LDLR) that is a receptor for ApoE proteins, is spliced at lower efficiency in males. Presumably due to this, the rs688(T;T) genotype was associated with increased risk for Alzheimer's disease odds in males (odds ratio 1.49, CI: 1.13-1.97, uncorrected p=0.005), but not in females. The presence of the rs688(T) allele associates with increased total and LDL-cholesterol in female members of the Framingham Offspring Study; rs688 was not associated with significant differences in HDL-cholesterol. The largest rs688-associated cholesterol differences were observed in pre-menopausal women. Taken together, rs688, a SNP present in approximately 60% of Caucasians, is associated with significant 10% in...
common in complete genomics
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Gene variants associated with deep vein thrombosis. Updated analysis of gene variants associated with deep vein thrombosis. per risk allele odds ratio *rs13146272 in CYP4V2 (risk allele frequency, 0.64) OR 1.24 (95% CI, 1.11-1.37) for rs13146272 *rs2227589 in SERPINC1 (risk allele frequency, 0.10) OR 1.29 (95% CI, 1.10-1.49) for rs2227589 *rs1613662 in GP6 (risk allele frequency, 0.84) OR 1.15 (95% CI, 1.01-1.30) for rs1613662 A study of 453 VTE cases and 1,327 controls was able to replicate the 'mild effects' of this SNP on risk for VTE, however they felt that stronger associations were found between increased VTE risk and either the Factor V Leiden mutation (rs6025)or having blood types O or A2. An evaluation of candidate genes of inflammation and thrombosis in relation to the risk of ve...
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rs2207418 is a SNP located in a 'gene desert' region of ch 20p12. In an Amish founder population of 851 individuals, the rs2207418(C) allele was associated with cardiac hypertrophy, increased risk of heart failure (relative risk 1.85, CI: 1.2 - 2.7, p = 0.0019), and increased mortality (hazard risk 1.5, CI: 1.2 - 1.9, p = 0.0004).
normal
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rs6280, also known as '''Ser9Gly''', is a SNP in the dopamine receptor D3 DRD3 gene. The rs6280(C) allele encodes a glycine, and the (T) allele encodes a serine (in dbSNP orientation). In a study of 88 patients being treated for schizophrenia with olanzapine, those who were rs6280(C;C) homozygotes had greater positive symptom remission (endpoint rating of minimal or none on all PANSS clinical response positive items, 39.1%), as compared with (C;T) or (T;T) genotypes (13.8%; p = 0.033). Ser9Gly has been implicated in executive function in some studies, but the results are conflicting. * Gly/Gly carriers showed significantly (p = 0.002) poorer performance than Ser/Ser carriers on executive functioning tasks in a somewhat small Caucasian sample (84 patients with first-episode psychosis and 85...
common in complete genomics
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Explaining variability in ciclosporin exposure in adult kidney transplant recipients. [PharmGKB:Curated risk allele: G; part of haplotype g.252A>G (rs1464603), g.275A>G (rs1464602), and g.4760G>A ; AF364606 significantly (P < .05) associated with oral midazolam clearance in the African American subpopulation (n = 14) but not in European Americans (n = 9).]
common in complete genomics
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[PharmGKB:Curated risk allele: G; part of haplotype g.252A>G (rs1464603), g.275A>G (rs1464602), and g.4760G>A ; AF364606 significantly (P < .05) associated with oral midazolam clearance in the African American subpopulation (n = 14) but not in European Americans (n = 9).]
normal
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rs1128503 is a SNP in the transporter P-glycoprotein (P-gp) 170, encoded by the ABCB1 (also known as MDR1) gene. Methadone is a substrate of this protein, so variants may affect the efficacy and optimal dosage of this drug as used for treating opiate dependence. A study of 98 methadone-maintaining patients concluded that the higher (>150 mg/day) and lower (< or =150 mg/day) methadone dose groups differed significantly in their rs1128503 status (experiment-wise p = 0.0325). Furthermore, individuals with the 3-locus genotype pattern (T;T)-(T;T)-(T;T) for SNPs rs1045642, rs2032582 and rs1128503, respectively, had an approximately 5-fold chance of requiring the 'higher' methadone dose, while individuals heterozygous for these three SNPs have an approximately 3-fold chance of stabilizing ...
common in complete genomics
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[PharmGKB:Curated This variant is the defining SNP for CYP3A7*2 which has increased catalytic acitivity compared to wild type.]
normal
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The rs2740574(G) allele encodes a variant form of CYP3A4 known as CYP3A4*1B. rs2740574(G) alleles are associated with an ~10 fold higher risk of aggressive prostate cancer in African American males. [PMID 16414488, OMIM A pooled study (1,400+ samples) along with a replication study conducted by members of the Ovarian Cancer Association Consortium found a 2.5-2.8x increased risk for ovarian cancer] for rs2740574(G;G) individuals (CI: 1.2-6.5, p=0.017). The authors note that CYP3A4 encodes a key enzyme in estrogen metabolism and which may be linked to ovarian carcinogenesis. [PharmGKB:Curated Risk or phenotype-associated allele: CYP3A4*1B, rs2740574 G allele. Phenotype: CYP3A4*1B (rs2740574 G) allele carriers show a significantly increased risk for SCLC (OR = 2.25, p = 0.02), which showed a...
normal risk
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rs1799983 (also known as Glu298Asp, E298D, or G894T) located in the NOS3 gene was associated with an ~2x risk (p=0.006) of developing pre-eclampsia (pregnancy-induced hypertension) and further complications of it in a study of ~50 African women. A large meta-analysis combining 26 studies (9,867 patients) found that homozygosity for rs1799983(T;T) increases risk of ischemic heart disease. The odds ratio was 1.31 (CI: 1.13-1.51). However, a study of 1,600 Greek patients concluded that rs1799983 was not associated with risk of acute myocardial infarction in that population. left ventricular hypertrophy in human essential hypertension OR=1.5 [PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: Women assigned to chemotherapy who had NOS3 −786 CC and 894 TT genotypes had a...
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rs1208 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1208(G). [PharmGKB:Curated in vitro study; PK: 20-fold reduction in Vmax vs wild type] [OMIM:?]
common in complete genomics Predicted to be a NAT2 slow metabolizer.
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With 99% sensitivity and 95% specificity, at least in Caucasian populations, rs1495741 is reported to classify the NAT2 phenotype of an individual; it therefore is a candidate to replace the 7-SNP panel used in genosets such as gs138, gs139, and gs140. The rs1495741(A;A), (A;G) and (G;G) genotypes predicted slow, intermediate, and rapid NAT2 acetylation phenotypes, respectively. [GWAS:None]
Magnitude: 0
Frequency: 4.4%
Repute:Good
References:118
Frequency: 4.4%
Repute:Good
References:118
Normal risk for type-2 diabetes
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rs13266634 is a SNP in the zinc transporter protein member 8 SLC30A8 gene that has primarily been associated with type-2 diabetes in several studies. This SNP is also known as the Arg325Trp or R325W variant; the (C) allele encodes the arginine (R), and the (T) allele encodes the tryptophan (W). significantly associated p = 0.0073; in 1,630 Japanese subjects with type-2 diabetes and in 1,064 controls The major alleles of the SLC30A8 SNP rs13266634 and the HHEX SNP rs7923837 associate with reduced insulin secretion, but not with insulin resistance. 46% of European non-diabetic offspring of type-2 diabetes patients are rs13266634(C;C) homozygotes; they are diabetes-prone and characterised by a 19% decrease in first-phase insulin release following an intravenous glucose load. * Note: this SNP,...
Magnitude: 0
Frequency: 48.7%
References:30
Frequency: 48.7%
References:30
average QT interval
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rs10494366, a SNP in the NOS1AP gene encoding the nitric oxide synthase I adaptor protein, accounts for some of the variation seen in abnormal heart rhythms, in particular, the QT interval. Based on studies totaling ~4,000 individuals of Caucasian ancestry, homozygotes for one allele have shorter QT intervals, while homozygotes for the other allele have a longer QT interval. A follow-up study determined that one rs10494366(G) allele was associated with a 3.8-ms (CI: 3.0 - 4.6ms, p=7.8x10(-20)) increase in QT interval duration, and two (G) alleles had twice that increase. No increase in risk for sudden death due to a cardiac problem was associated with this SNP, though. rs10494366 minor homozygotes had a 9.3 msec longer QT interval compared to major homozygotes (p=5.7x10(-5)); rs10918594 mi...
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rs2165870 is a SNP in or near the promoter region of the muscarinic acetylcholine receptor 3 subtype CHRM3 gene on ch 1. A GWAS study of 300+ patients exhibiting post-operative nausea found that carriers of rs2165870(A) alleles were at 2.3x higher risk for nausea (CI: 1.36 - 4, p = 0.002). rs2355230 is said to be a perfect proxy (r2 = 1) for rs2165870.
common in clinvar
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Technology to accelerate pangenomic scanning for unknown point mutations in exonic sequences: cycling temperature capillary electrophoresis (CTCE). Genetic variation in the one-carbon transfer pathway and ovarian cancer risk. Strong association of a common dihydropyrimidine dehydrogenase gene polymorphism with fluoropyrimidine-related toxicity in cancer patients. Genetic variation in TYMS in the one-carbon transfer pathway is associated with ovarian carcinoma types in the Ovarian Cancer Association Consortium. [PharmGKB:Curated Patients heterozygous for the C allele of this SNP exhibited increased incidence of medium-severe nausea and vomiting (as defined by WHO criteria) relative to those carrying only the T allele. The patient population consisted of individuals with gastric or colon ca...
common in complete genomics
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[PharmGKB:Curated The C allele of this variant was associated with increased risk of toxicity in African American Rheumatoid Arthritis patients receiving methotrexate.]
0.5x decreased risk for endometriosis
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rs1800871(C) carriers are associated with a reduced endometriosis risk by approximately 2x compared with the common rs1800871(T;T) genotype in a study of 196 Chinese patients. rs2222202 (C/T) (p=0.03) and rs1800871 (C/T) (p=0.05) showed significant allelic associations with pediatric onset Crohn's disease. rs1800871(T) carriers were 3x more likely to have their pregnancies terminate early (<10 weeks) than (C) carriers, based on a study of ~500 pregnancies. In a study of 1,757 cases of Alzheimer's disease and 6,295 controls, an interaction was replicated between IL6 genotype rs2069837(A;A) and IL10 genotype rs1800871(C;C). The synergy factor (SF) was 1.63 (CI: 1.10-2.41, p = 0.01), controlling for age, gender and ApoE4 genotype. 23andMe reports that each G allele at rs1800871 is associat...
normal/common
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rs6025 represents a SNP in the Factor V F5 gene, encoding a change in the protein from an arginine at position 506 to a glutamine. The resulting rs6025(A) allele encodes a mutation known as the Leiden mutation, R506Q, found in perhaps 3 to 5% of the individuals in most populations. About 1 in 10 individuals harboring the R506Q will experience clinically significant venous thromboembolism in their lifetimes (according to OMIM). Overall, the rs6025(A) allele appears to be necessary but not sufficient for the development of venous thromboembolism. Patients who are rs6025(A;G) heterozygotes but lack other risk-enhancing SNPs have a risk of recurrent deep venous thrombosis equal to patients with no such SNPs. In contrast, patients who are heterozygotes for both rs6025 and the prothrombin rs1799...
normal
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rs396991 is a SNP in the Fc fragment of IgG, low affinity IIIa, receptor (CD16a) FCGR3A gene. rs396991(T) encodes the phenylalanine (F) allele, with the (G) allele encoding the variant valine (V). The (V) isoform is considered high-binding to IgG1 and IgG3, while the (F) isoform is considered low-binding. This SNP is known in the literature by many names, including A559C, T559G, 158F/V, and 176F/V. What's the importance of this? FcgRIIIa stimulatory receptors are expressed by most cells in the immune system, including monocytes, dendritic cells, macrophages, natural killer cells, platelets and endothelial cells, as well as a subpopulation of T-cells. FcgR isoforms have been linked to the pathogenic consequences triggered by autoantibodies or immune complexes in autoimmune diseases such as ...
common in complete genomics
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Although somewhat lacking in statistical power, several reports have linked rs1205, a UTR mutation known as CRP4 in the C-reactive protein CRP to the autoimmune disorder SLE, systemic lupus erythematosus. The risk allele in dbSNP orientation is (T). C-reactive protein (CRP) levels obesity rs1205(G) allele had significantly higher CRP levels than noncarriers in a dose-dependent manner suggesting a possible association with fat localization 23andMe blog each rs1205(T) lowered CRP by 20% but no association with heart disease. Analysis of polymorphisms in 16 genes in type 1 diabetes that have been associated with other immune-mediated diseases. A prospective assessment of the Y402H variant in complement factor H, genetic variants in C-reactive protein, and risk of age-related macular degenerat...
common
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rs7566605 was initially reported as being associated in at least 4 independent populations as being associated with obesity however replications are inconsistent, and a recent (2009) large meta-analysis comprising 34 studies (and over 70,000 subjects) has concluded that there is no evidence for overall association of the rs7566605 polymorphism with obesity. See also: Poster At least one population has since been reported in which this association was not seen. Furthermore, a study of 18,000 Danish subjects also failed to find any direct role for this SNP in the development of obesity, except that among physically inactive subjects, (C)-allele carriers tended to have a higher body mass index (by O.5 kg/m2) than (G)-allele carriers. On the other hand, a report has also been published indicat...
Normal risk for autoimmune disorders
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This SNP, located in the PTPN22 gene and also known as R620W, or 1858C>T, may influence Rheumatoid Arthritis and other autoimmune diseases, including but not limited to, multiple sclerosis, Crohn's disease, celiac disease and type-1 diabetes. In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for type-1 diabetes for this SNP was recalculated to be 1.98 (CI 1.82-2.15). rs2476601 was confirmed in another 2007 study to be a risk factor for RA . * confirms the association of rs2476601 rheumatoid arthritis * two copies of the PTPN22 R620W allele more than doubles the risk for RF positive RA * see rs2476601(A;G) * * * * * rs2476601 shows a 0.75 (r squared) correlation with rs6679677, a SNP in the RSBN1 gene associated with rheumatoid arthritis...
common
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rs6427528 is a SNP in the chromosome 1q23 region apparently located near enough to the CD84 locus to affect it's expression. A GWAS study of 2,700+ rheumatoid arthritis (RA) patients treated with one of three anti-TNF drugs found that rs6427528(A) carriers had higher CD84 expression and responded better to etanercept treatment. The effect was statistically significant but not that large in magnitude, totaling 2.6% of the variance in response to etanercept treatment. The result was seen in European (Caucasian) patients, but perhaps due to small patient numbers, was not statistically supported in Japanese patients. [GWAS:Response to anti-TNF treatment in rheumatoid arthritis]
normal
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rs4673, also known as C242T or H72Y, is a SNP in the NAD(P)H oxidase p22(phox) subunit CYBA gene. A study of German patients with ischemic stroke or transient ischemic attack under the age of 50 (n = 161) concluded that rs4673(T;T) individuals were almost 4 times more likely to experience cerebral ischemia (odds ratio 3.85, CI: 1.39-10.64) compared to rs4673(C;T) or (C;C) individuals after adjusting for classical risk factors. A meta-analysis concluded that the T allele effect may vary between ethnicities in both direction of effect and significance; Asian populations may have reduced coronary artery disease risk associated with the T allele. Genetic polymorphisms and susceptibility to lung disease. Genetic association of glutathione peroxidase-1 with coronary artery calcification in type ...
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G allele associated with schizophrenia among 120 (likely Japanese) first-episode neuroleptic-naive schizophrenics treated with risperidone genotyped for 30 variants in misc. dopamine and serotonin (receptors and otherwise) two SNPs in DRD2 (rs1799989 and rs1800497) and two SNPs in AKT1 (rs3803300 and rs2494732) were significant predictors of treatment response to risperidone The ancestral allele is G in the dbSNP database. [PharmGKB:Curated This SNP is significant predictor of treatment response to risperidone in first-episode schizophrenia.]
normal
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rs2542151 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.3 (CI 1.14-1.48), and for homozygotes, 2.01 (CI 1.46-2.76). rs2542151 has been reported in the same study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.30 (CI 1.15-1.47), and for homozygotes, 1.62 (CI 1.17-2.24). In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for this SNP was recalculated to be 1.30 (CI 1.22–1.40). [PharmGKB:Non-Curated GWAS results: Meta-analysis of genome-wide association study data identifies additional type 1 diabete...
better response to inhaled corticosteroid in patients with COPD
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rs242941 is a SNP in the corticotrophin-releasing hormone receptor 1 CRHR1 gene. (G;G) better response to inhaled corticosteroids fluticasone propionate and salmeterol in patients with COPD in a Korean study with 84 subjects. [PharmGKB:Curated Haplotype tagging SNP.]
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rs2227956 in HSP70-hom, resulted in a significant association with noise-induced hearing loss [PharmGKB:Curated The C allele of this SNP is part of a haplotype that has been associated with protection from hypersensitivity to carbamazepine.] [OMIM:?]
normal
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(C;C) predisposes to papillary thyroid carcinoma. Among 42 patients with familial breast cancer and 82 patients with ovarian cancer, those with at least one rs2910164(C) SNP tended to have been diagnosed at an earlier age than those with only (G) alleles. For the breast cancer patients, the difference in median age was between 45 vs 56 (p = 0.029) and for ovarian cancer patients, 45 vs 50, (p = 0.014). (G;G) males were two-fold more susceptible to hepatocellular carcinoma (OR = 2.016, 95% CI = 1.056-3.848, P = 0.034) perhaps an ambiguous flip? [OMIM:MICRO RNA 146A; MIRN146A]
normal
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rs699947 (-2578C>A) is a SNP within close proximity of VEGFA (Vascular endothelial growth factor A). The A allele of rs699947 increased a risk for thyroid cancer (adjusted OR=1.36, 95% C.I=1.02~1.81, P=0.039) and regional lymph node metastasis only in men. [PharmGKB:Curated Risk or phenotype-associated allele: CA. Phenotype: Response was observed in 21% of the patients with the -2578 CA genotype compared with 59% of the patients with CC+AA. This genotype was also associated with poor progression free survival (PFS). Study size: 72. Study population/ethnicity: Patients with metastatic colorectal neoplasms; Denmark. Significance metric(s): p = 0.002 (response); HR = 1.74, CI 1.04-2.92, p = 0.02 (PFS) Type of association: PD; CO] [OMIM:?]
common on affy axiom data
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nortriptyline response [PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: The SNP within an intron of the uronyl 2-sulphotransferase gene was associated with outcome at a genome-wide level of significance and with a very small posterior probability of being a false positive. Carriers of the minor A allele experienced less improvement of depression symptoms than carriers of the GG homozygote from week 4 onward. Study size: 312 Study population/ethnicity: Individuals with unipolar depression of at least moderate severity treated with nortriptyline. Type of association: GN] [GWAS:Response to antidepressants]
normal Rs3135388(C;C) is highly correlated with the HLA-DRB1*1501 allele. There is no additional risk of multiple sclerosis associated with the (C;C) genotype.
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rs3135388(T) is highly (> 99%) correlated with the HLA-DRB1*1501 allele; the risk allele (T) is associated with a 3 to 6 fold higher risk for developing multiple sclerosis. The risk per allele (or per haplotype) appears additive. It has also been associated with other autoimmune diseases, such as systemic lupus erythematosis (SLE) (see) and, when linked with DQB1*0602, narcolepsy. The HLA-DRB1*1501 allele is fairly common; for example, it occurs in 15-30% of individuals of Northern European ancestry. Note: most publications refer to the risk allele as rs3135388(A), but in dbSNP and SNPedia orientation, it is rs3135388(T). An interesting series of correlations have been woven together to suggest that a possible way to lower the risk of rs3135388(T) carriers developing multiple sclerosis ...
normal
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In Caucasian non-Hispanics, the rs1360780(T) allele is associated with increased risk for depression, with an odds ratio of 1.39 (CI: 1.14-1.70, p=0.046). This same SNP, which is in the FKBP5 gene, may influence how patients respond to antidepressants including citalopram. rs1360780(T;T) homozgyotes tend to report more depressive episodes, but they also respond better to treatment with antidepressants. rs9296158 rs3800373 rs1360780 rs9470080 linked with the severity of child abuse to predict level of adult PTSD symptoms after correcting for multiple testing. [PharmGKB:Curated This variant is associated with higher chance of response to anti-depressant drugs.] [OMIM:FK506-BINDING PROTEIN 5; FKBP5]
normal
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rs1801394, also known as A66G or Ile22Met, is a SNP in the methionine synthase MTRR gene. This gene encodes one of the two enzymes involved in the production of methionine (the other is MTR). The protein encoded by an rs1801394 allele has a lower affinity for MTR () and is inconsistently associated with homocysteine level, although it is a risk factor for neural tube defects () and Down syndrome () in conditions of higher homocysteine. Based on a study of British patients with primary brain tumors, (1,005 glioma cases and 631 meningioma cases), rs1801394(G;G) individuals were at higher risk for meningioma (odds ratio 1.41, CI: 1.02-1.94). In general, genotypes associated with increased 5,10-methylenetetrahydrofolate levels are associated with elevated risk for these types of brain cancer. ...
common in complete genomics
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[PharmGKB:Curated The G allele of this polymorphism is associated with the intensification of nicotine dependence in a genetic association study in three large samples from the German general population (N1=1412; N2=1855; N3=2294). This variant is in the 3'-untranslated region of CHRNA4 gene.] [OMIM:CHOLINERGIC RECEPTOR, NEURONAL NICOTINIC, ALPHA POLYPEPTIDE 4; CHRNA4]
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Variation at this SNP, rs2298383, appears to influence how an individual responds to moderate levels (150mg) of caffeine. [PharmGKB:Curated Risk or phenotype-associated allele: rs2298383 T allele. Phenotype: Carriers of 1 or 2 copies of the T allele for rs2298383 showed increased risk of any (OR = 2.23, CI 1.03-5.07, p = 0.03) or gastrointestinal-specific (OR = 2.65, CI = 0.8-11.35, p = 0.09) adverse events. Study size: 309 RA patients, including 147 good MTX responders, 101 MTX inefficacy failures, and 61 adverse event (AE) MTX failures (e.g. gastrointestinal (n = 24), abnormal liver function tests (n = 20), haematological (n = 7), skin rashes (n = 6), and other (n = 17). Study population/ethnicity: Rheumatoid arthritis (RA) patients aged over 18 yrs, of White Caucasian ethnic origin, cl...
None
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Variation at this SNP, rs5751876, also referred to as 1976C>T or 1976T>C, appears to influence how an individual responds to moderate levels (150mg) of caffeine. T/T carriers displaying significantly increased subjective levels of anxiety after consumption. However a PharmGKB variant annotation suggests it is (C;C) genotypes who are more sensitive to caffeine. rs5751876 is not associated with how much coffee one drinks, though, nor with risk for Parkinson's disease, based on a study of 1,200 subjects. 'rs2298383 shows functional potential based on in silico analyses and might therefore represent the true underlying causal variant'
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Variation at this SNP, rs4822492, appears to influence how an individual responds to moderate levels (150mg) of caffeine.
normal
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This SNP, located in an intron of the GRIA3 gene (also known as AMPA3), has been linked in one study to increased thoughts of suicide in patients taking the anti-depressant drug citalopram. The increased risk is calculated to be 1.9x. If the individual is also carrying two rs2518224(C) alleles, i.e. is a rs2518224(C;C) homozygote, the odds ratio for having suicidal thoughts is increased to ~15x (CI: 3.7 - 60.6). [PharmGKB:Curated This SNP in the GRIA3 gene was associated with treatment-emergent suicidal ideation during citalopram therapy in a clinically representative cohort of outpatients with major depressive disorder. DNA samples from 1,915 participants were genotyped.]
798 snps
(hide) Placebo
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rs4570625 and rs4565946 linked to the pathogenesis of early-onset obsessive compulsive disorder Tourette's Syndrome
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower COMT enzymatic activity, therefore higher dopamine levels; lower pain threshold, enhanced vulnerability to stress, yet also more efficient at processing information under most conditions *rs4680(G) = Warrior. Val, less exploratory, higher COMT enzymatic activity, therefore lower dopamine levels; higher pain threshold, better stress resiliency, albeit with a modest reduction in executive cognition performance under most conditions Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis; summary at ) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compar...
2 snps
(hide) Pregnancy
1.3x increased risk for type-2 diabetes
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The accuracy of claims about this snp are called into question by table 1 of discusses the process of including this snp into Coriell and raises some doubt about the value of its inclusion. rs7754840 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.28 (CI: 1.17-1.41, p = 4.5 x 10e-7) type-2 diabetes Carriers of the (C;G) and (C;C) genotypes of rs7754840 had 11% and 24% lower first-phase insulin release in an IVGTT compared to that in carriers of the (G;G) genotype (P=0.002). The C allele was also associated with higher glucose area under the curve in an OGTT (P=0.016). rs7754840 type-2 diabetes Ashkenazi Jewish population shows an even stronger effect for rs7754840 than the general Caucasian population, based on 1,131 cases versus 1,147 co...
Avg. fasting Plasma Glucose 5.18 mmol/L (93 mg/dl). Slightly higher blood glucose. Fasting Plasma Glucose is the amount of sugar in your blood when you wake up. It's required to power your body, but too much is very bad for you. Fasting plasma glucose between 5.6 mmol/L and 6.9 mmol/L (101 – 125 mg/dl) is considered pre-diabetes. Fasting plasma glucose higher than 7 mmol/L (126 mg/dl) is considered diabetes.
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rs560887, p = 4 x 10(-7)) *654 normoglycemic subjects, replicated in 9,353 subjects *fasting plasma glucose (FPG) (beta = -0.06 mmol/l per A-allele, combined p = 4 x 10(-23)) and with pancreatic beta-cell function (Homa-B model, combined p = 3 x 10(-13)) in three populations; however it was not associated with type 2 diabetes risk. (ageing) Blood Glucose [PharmGKB:Non-Curated Phenotype 1: In a meta-analysis of 21 GWAS cohorts followed by analysis in additional individuals, this SNP was found to be associated with fasting glucose level. Study size: 119,169. Significance metric(s): p = 8.7 x 10(-218). Phenotype 2: In the same study, this SNP was found to be associated with HOMA-B (homeostasis model assessment of beta-cell function). Study size: 94,839. Significance metric(s): p = 1.5 x 10(-...
1.2x increased risk for type-2 diabetes
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rs4402960 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.23 (CI: 1.11-1.36, p = 8.1 x 10e-5) associated with type-2 diabetes significantly associated with type-2 diabetes p = 0.00009; in 1,630 Japanese subjects and in 1,064 controls 1,638 type-2 diabetes patients and 1,858 controls *rs4402960 borderline (OR 1.10, 95% CI: 0.99-1.22). Neither rs4402960 or rs1470579 were found to be associated with type-2 diabetes in a study of 3,000 French Caucasians. This SNP was confirmed to be associated with type-2 diabetes in a study of 500+ Japanese patients plus pooled meta-analysis with 6 previous association studies (also of Japanese). Note: rs4402960 is fairly tightly linked (r<sup>2</sup>=0.87) with another IGF2BP2 gene SNP also asso...
increased risk of hypertension
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rs699 is a SNP in the angiotensin AGT gene that encodes a functional change. In most published literature, the name for this SNP is M235T, or perhaps Met235Thr, however its amino acid 268 (not 235) that varies based on the numbering in todays databases. rs699 is also occasionally known as C4072T. In any case, the rs699(C) allele encodes the threonine variant, which is associated with higher plasma angiotensin levels, and ultimately higher blood pressure leading to increased risk for hypertension associated disorders. This association was first reported in 1992 , and many studies, though not all, have replicated these findings. rs699 is also (generally) reported to be in tight linkage with rs5051, a neighboring SNP in the promoter of the AGT gene. rs699(C) has also been implicated as a risk...
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[GWAS:Glycemic traits (pregnancy)]
1.6x risk for ICP
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rs3740066, a SNP in the ABCC2 gene, is reported to be associated with a higher risk of developing intrahepatic cholestasis of pregnancy (ICP) based on a study of ~70 Argentinian patients. ICP is associated with increased fetal risks such as premature birth or intrauterine death. The risk allele is rs3740066(A), and the odds ratio for homozygous rs3740066(A;A) mothers is 4.44 (CI: 1.83 - 10.78), and for heterozygous mothers 1.65 (CI: 0.76 - 3.64), compared to rs3740066(G;G) mothers. [PharmGKB:Curated The AUCs of irinotecan, SN-38, SN-38 glucuronide, and APC are influenced by rs3740066, rs2306283, rs35605, rs10276036, and rs717620 .]
Frequency: 43.4%
References:1
References:1
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[GWAS:Preeclampsia]
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Women with the snp has been linked to significant risk of a premature birth These press releases explain it more simply The risky variation is 3x more common in women of african descent. *rs2298668 Prolylcarboxypepdiase E112D (rs2298668)D allele alone and jointly with chronic hypertension were associated with a significantly increased risk of preeclampsia Polymorphism in maternal LRP8 gene is associated with fetal growth.
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[GWAS:Preeclampsia]
1.9x risk for pre-eclampsia
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rs4762, a SNP in the angiotensin II AGT gene, has been reported to be associated with increased risk for developing pre-eclampsia, based on a study of ~180 French-Canadian women. The odds ratio associated with the rs4762(T) allele (encoding methionine) was 1.9 (CI:1.2–2.9, p=0.0033). Note that rs4762 is commonly referred to in the literature as 'T174M' or 'Thr174Met'; however, databases now indicate that the amino acid that varies is #207 (not 174), as the protein is currently numbered. rs4762 was also reported to play the major role in the 2.1 fold increased risk (CI: 1.4-3.4, p=0.0008) for pre-eclampsia of the rs3889728(A)-rs4762(T)-rs699(C) haplotype. Correction of population stratification in large multi-ethnic association studies. Ten renin-angiotensin system-relate...
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[GWAS:Preeclampsia]
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[GWAS:None]
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preterm birth rs4696480 (T-16934A and Arg753Gln) and rs5743708) (Thr399Ile) earlier birth for infants carrying two (-16934TA/AA and 753ArgGln/GlnGln)
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A variant upstream of the CDH13 adiponectin receptor gene and metabolic syndrome in Swedes. Dissecting complex traits: recent advances in hypertension genomics. [PharmGKB:Non-Curated GWAS results: Genome-wide scan identifies CDH13 as a novel susceptibility locus contributing to blood pressure determination in two European populations. (Initial Sample Size: 364 cases, 590 controls; Replication Sample Size: 1,043 cases, 1,769 controls); (Region: 16q23.3; Reported Gene(s): CDH13; Risk Allele: rs11646213-T); (p-value= 0.000008).This variant is associated with Hypertension.] [GWAS:Hypertension]
References:1
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[GWAS:Preeclampsia]
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[GWAS:Preeclampsia]
normal
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rs5219, also known as E23K, is a SNP in the KCNJ11 gene. The association between type-1 diabetes and rs5219 is mentioned as being replicated in ; there is also a 90% correlation between rs5219 and rs5215. This SNP is one of 4 relatively common SNPs reported to represent risk for type-2 diabetes in the DESIR prospective study of 3,877 Caucasian participants. Under an additive model, the odds ratio for the minor (risk) allele (T) is 1.15 (CI: 0.95-1.4, p=0.2, ie not significant). But for the 4 SNPs, each risk allele increased type-2 diabetes risk by 1.34x (p=2x10e-6), with an odds ratio of 2.48 (CI: 1.59-3.86) for carriers of 4 or more compared to those with one or none (risk alleles). Genotyping of ~4000 Chinese as well a meta-analysis concluded that rs5219 was associated with type-2 diabet...
normal risk
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rs1799983 (also known as Glu298Asp, E298D, or G894T) located in the NOS3 gene was associated with an ~2x risk (p=0.006) of developing pre-eclampsia (pregnancy-induced hypertension) and further complications of it in a study of ~50 African women. A large meta-analysis combining 26 studies (9,867 patients) found that homozygosity for rs1799983(T;T) increases risk of ischemic heart disease. The odds ratio was 1.31 (CI: 1.13-1.51). However, a study of 1,600 Greek patients concluded that rs1799983 was not associated with risk of acute myocardial infarction in that population. left ventricular hypertrophy in human essential hypertension OR=1.5 [PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: Women assigned to chemotherapy who had NOS3 −786 CC and 894 TT genotypes had a...
normal/common
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rs6025 represents a SNP in the Factor V F5 gene, encoding a change in the protein from an arginine at position 506 to a glutamine. The resulting rs6025(A) allele encodes a mutation known as the Leiden mutation, R506Q, found in perhaps 3 to 5% of the individuals in most populations. About 1 in 10 individuals harboring the R506Q will experience clinically significant venous thromboembolism in their lifetimes (according to OMIM). Overall, the rs6025(A) allele appears to be necessary but not sufficient for the development of venous thromboembolism. Patients who are rs6025(A;G) heterozygotes but lack other risk-enhancing SNPs have a risk of recurrent deep venous thrombosis equal to patients with no such SNPs. In contrast, patients who are heterozygotes for both rs6025 and the prothrombin rs1799...
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[GWAS:Preeclampsia]
21 snps
(hide) QT interval
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23andMe blog Influences QT interval [PharmGKB:Non-Curated GWAS results: Common variants at ten loci influence QT interval duation in the QTGEN Study. (Initial Sample Size: 13,685 individuals; Replication Sample Size: 15,854 individuals); (Region: 11p15.5; Reported Gene(s): KCNQ1; Risk Allele: rs2074238-T); (p-value= 0.00000000000000003).This variant is associated with QT interval.] [GWAS:QT interval]
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[GWAS:QT interval]
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[GWAS:QT interval]
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[GWAS:QT interval]
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[PharmGKB:Non-Curated GWAS Results: Whole genome association study identifies polymorphisms associated with QT prolongation during iloperidone treatment of schizophrenia (Initial Sample Size: 183 individuals; Replication Sample Size: NR; Risk Allele: rs7142881-A). This variant is associated with Response to iloperidone treatment (QT prolongation).] [GWAS:Response to iloperidone treatment (QT prolongation)]
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[PharmGKB:Non-Curated GWAS Results: Whole genome association study identifies polymorphisms associated with QT prolongation during iloperidone treatment of schizophrenia (Initial Sample Size: 183 individuals; Replication Sample Size: NR; Risk Allele: rs4799915-T). This variant is associated with Response to iloperidone treatment (QT prolongation).] [GWAS:Response to iloperidone treatment (QT prolongation)]
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[GWAS:QT interval]
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rs10494366, rs4657139 and rs16847548 were significantly associated with adjusted QT interval in whites. relative hazard of SCD associated with each C allele at rs16847548 was 1.31. rs12567209 was also independently associated with SCD in whites (relative hazard 0.57, 95% confidence interval 0.39 to 0.83, P=0.003). No significant associations observed in blacks.
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[GWAS:QT interval]
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QT interval rs3807375 rs2880058 [PharmGKB:Curated QT prolongation] [GWAS:Electrocardiographic traits]
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[GWAS:QT interval]
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23andMe blog Influences QT interval [PharmGKB:Non-Curated GWAS results: Common variants at ten loci influence QT interval duation in the QTGEN Study. (Initial Sample Size: 13,685 individuals; Replication Sample Size: 15,854 individuals); (Region: 7q36.1; Reported Gene(s): KCNH2; Risk Allele: rs4725982-T); (p-value= 0.0000000000000005).This variant is associated with QT interval.] [GWAS:QT interval]
References:1
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[GWAS:QT interval]
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[GWAS:QT interval]
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[GWAS:QT interval]
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[GWAS:QT interval]
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[GWAS:QT interval]
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[GWAS:QT interval]
Frequency: 9.7%
References:4
References:4
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23andMe blog Influences QT interval [PharmGKB:Non-Curated GWAS results: Common variants at ten loci influence QT interval duation in the QTGEN Study. (Initial Sample Size: 13,685 individuals; Replication Sample Size: 15,854 individuals); (Region: 3p22.2; Reported Gene(s): SCN5A; Risk Allele: rs12053903-C); (p-value= 0.00000000000001).This variant is associated with QT interval.] [GWAS:QT interval]
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[GWAS:QT interval]
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New atypical antipsychotics for schizophrenia: iloperidone. [PharmGKB:Non-Curated GWAS Results: Whole genome association study identifies polymorphisms associated with QT prolongation during iloperidone treatment of schizophrenia (Initial Sample Size: 183 individuals; Replication Sample Size: NR; Risk Allele: rs993648-T). This variant is associated with Response to iloperidone treatment (QT prolongation).] [GWAS:Response to iloperidone treatment (QT prolongation)]
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[GWAS:QT interval]
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23andMe blog Influences QT interval [PharmGKB:Non-Curated GWAS results: Common variants at ten loci influence QT interval duation in the QTGEN Study. (Initial Sample Size: 13,685 individuals; Replication Sample Size: 15,854 individuals); (Region: 16p13.13; Reported Gene(s): LITAF,CLEC16A, SNN, ZC3H7A, TNFRSF17; Risk Allele: rs8049607-T); (p-value= 0.000000000000005).This variant is associated with QT interval.] [GWAS:QT interval]
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[PharmGKB:Non-Curated GWAS results: Common variants at ten loci modulate the QT interval duration in the QTSCD Study. (Initial Sample Size: 15,842 individuals; Replication Sample Size: up to 13,602 individuals); (Region: 16q21; Reported Gene(s): NDRG4; Risk Allele: rs7188697-A); (p-value= 7E-25).This variant is associated with QT interval.] [GWAS:QT interval]
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[GWAS:QT interval]
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23andMe blog Influences QT interval [PharmGKB:Non-Curated GWAS results: Common variants at ten loci influence QT interval duation in the QTGEN Study. (Initial Sample Size: 13,685 individuals; Replication Sample Size: 15,854 individuals); (Region: 17q12; Reported Gene(s): LIG3,RFFL; Risk Allele: rs2074518-T); (p-value= 0.000000000006).This variant is associated with QT interval.] [GWAS:QT interval]
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23andMe blog Influences QT interval DNA repair and cell cycle control genes and the risk of young-onset lung cancer. Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival. Genetic variation in immune regulation and DNA repair pathways and stomach cancer in China.
Frequency: 42.5%
References:3
References:3
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Common variants at ten loci influence QT interval duration in the QTGEN Study. [PharmGKB:Non-Curated GWAS results: Common variants at ten loci modulate the QT interval duration in the QTSCD Study. (Initial Sample Size: 15,842 individuals; Replication Sample Size: up to 13,602 individuals); (Region: 17q24.3; Reported Gene(s): KCNJ2; Risk Allele: rs17779747-T); (p-value= 0.000000000006).This variant is associated with QT interval.] [GWAS:QT interval]
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[GWAS:QT interval]
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[GWAS:QT interval]
common in complete genomics
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[PharmGKB:Non-Curated GWAS Results: Whole genome association study identifies polymorphisms associated with QT prolongation during iloperidone treatment of schizophrenia (Initial Sample Size: 183 individuals; Replication Sample Size: NR; Risk Allele: rs4933824-T). This variant is associated with Response to iloperidone treatment (QT prolongation).] [GWAS:Response to iloperidone treatment (QT prolongation)]
Magnitude: 0
Frequency: 48.7%
References:30
Frequency: 48.7%
References:30
average QT interval
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rs10494366, a SNP in the NOS1AP gene encoding the nitric oxide synthase I adaptor protein, accounts for some of the variation seen in abnormal heart rhythms, in particular, the QT interval. Based on studies totaling ~4,000 individuals of Caucasian ancestry, homozygotes for one allele have shorter QT intervals, while homozygotes for the other allele have a longer QT interval. A follow-up study determined that one rs10494366(G) allele was associated with a 3.8-ms (CI: 3.0 - 4.6ms, p=7.8x10(-20)) increase in QT interval duration, and two (G) alleles had twice that increase. No increase in risk for sudden death due to a cardiac problem was associated with this SNP, though. rs10494366 minor homozygotes had a 9.3 msec longer QT interval compared to major homozygotes (p=5.7x10(-5)); rs10918594 mi...
Magnitude: 0
References:0
References:0
35 snps
(hide) Revised NEO Personality Inventory
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[PharmGKB:Non-Curated GWAS results: Genome-wide association scan for five major dimensions of personality. (Initial Sample Size: 3,972 individuals; Replication Sample Size: 3,903 individuals); (Region: 19q13.31; Reported Gene(s): ZNF180; Risk Allele: rs644148-G); (p-value= 0.0000009).This variant is associated with Personality dimensions(openness).] [GWAS:Personality dimensions]
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The G allele of SNAP25 gene SNP rs362584 was associated with increased neurotic traits (combined p value = 0.0000522) in a group of 3972 Sardinians, and two smaller replicative samples from the USA and Netherlands (the replicative samples were not significant by themselves, with the Netherlands sample showing considerably less of a trend).full paper in pdf
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The A allele of the CLOCK gene SNP rs6832769 was associated with lessened agreeableness (p = 0.00000871) in a group of 3972 Sardinians. The effect remained significant in the replicative American sample, but failed to achieve significance in the Norwegian sample and third sample (though the combined p value remained significant at 0.000865). full paper in pdf [PharmGKB:Non-Curated GWAS results: Genome-wide association scan for five major dimensions of personality. (Initial Sample Size: 3,972 individuals; Replication Sample Size: 3,903 individuals); (Region: 4q12; Reported Gene(s): CLOCK; Risk Allele: rs6832769-A); (p-value= 0.000002).This variant is associated with Personality dimensions.]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association scan for five major dimensions of personality. (Initial Sample Size: 3,972 individuals; Replication Sample Size: 3,903 individuals); (Region: 2p22.1; Reported Gene(s): THUMPD2; Risk Allele: rs2540226-T); (p-value= 0.000003).This variant is associated with Personality dimensions.] [GWAS:Personality dimensions]
4 snps
(hide) SERPINA1
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finds no association between rs11832 and pulmonary emphysema
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[OMIM:PI M1-VAL213]
Frequency: 17.0%
References:1
References:1
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finds no association between rs17751769 and pulmonary emphysema
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finds no association between rs8004738 and pulmonary emphysema
7 snps
(hide) Skin color
Generally European; Light skin; Possibly an increased risk of melanoma This SNP is associated with skin, hair, and eye colour, and risk of melanoma. Individuals with the G;G genotype are generally of European descent and have fair skin. In a population-based case-control study investigating a number of pigmentation-related SNPs and their correlation with cutaneous malignant melanoma (CMM) in a Caucasian Australian population, rs16891982 (variant F374L) was found to be associated with odds ratios of 3.44, 2.86, 1.68, and 1.68 for all study subjects (1,738 CMM cases and 4,517 controls); subjects with northern European ancestry (1,438 cases and 3,098 controls); northern European subjects adjusted for hair, eye, and skin colour; and northern European subjects adjusted for the MC1R genotype, r...
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This snp influences skin pigmentation. The allele p.L374F indicates light-skinned european ancestry c.1122C>G, p.Phe374Leu (NCBI dbSNP rs16891982) in SLC45A2 was associated with protection from malignant melanoma (OR, 0.41; 95% CI, 0.24-0.70; P=0.008 after adjustment for multiple testing) An association study conducted on a population of European origin concluded that the rare (in Europeans, at least) allele L374, i.e. rs16891982(C) in dbSNP orientation, significantly increases the possibility of having black hair color, with an odds ratio of around 7. This population-based case-control study investigated a number of pigmentation-related SNPs and their correlation with cutaneous malignant melanoma (CMM) in an Australian population. rs16891982 (variant F374L) was found to be associated w...
1 snp
(hide) SLC6A2
may be associated with ADHD
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T allele may be associated with Attention deficit hyperactivity disorder.
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Pharmacogenetics of antidepressant response.
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Trajectories of change in depression severity during treatment with antidepressants. Pharmacogenomics of antidepressant drugs.
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A allele associated with better response to treatment of ADHD with atomoxetine.
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G allele associated with better response to treatment of ADHD with atomoxetine.
common in complete genomics
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T allele associated with better response to treatment of ADHD with atomoxetine.
12 snps
(hide) Test Trails A
Frequency: 43.4%
References:1
References:1
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non sig. gwas, hit (p = 4 x 10^-6) for Trails A performance [GWAS:Cognitive Performance]
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non sig. gwas, hit (p = 4 x 10^-6) for Test Trails A performance [GWAS:Cognitive Performance]
Frequency: 40.0%
References:1
References:1
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non sig. gwas, hit (p = 4 x 10^-6) for Trails A performance [GWAS:Cognitive Performance]
3 snps
(hide) Tetrahydrobiopterin
increased risk of autism Increased risk of autism.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2784255/]
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Examination of tetrahydrobiopterin pathway genes in autism. Examination of association to autism of common genetic variation in genes related to dopamine.
1 snp
2 snps
(hide) TPMT
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: Not specified. Phenotype: This SNP was associated with clearance of docetaxel. Study size: 31. Study population/ethnicity: Patients with Non-Small-Cell Lung Carcinoma. Significance metric(s): p = 0.1013 (ANOVA); p = 0.0159 (QMIS); p = 0.0178 (KW) Type of association: PK.]
1 snp
(hide) Triglycerides
slightly higher risk for gout
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The T allele of rs1260326 has been associated with type 2 diabetes and hypertriglyceridemia. A fine mapping approach indicates that this SNP, rs1260326, shows the strongest association signal with metabolic phenotypes in the region that also harbors the tightly linked (r(2)=0.93) SNP rs780094, which has been previously associated with triglyceride and glucose concentrations. This SNP, rs1260326, encodes a common missense glucokinase regulatory protein gene GCKR variant. gout association, based on Loci related to metabolic-syndrome pathways including LEPR,HNF1A, IL6R, and GCKR associate with plasma C-reactive protein: the Women's Genome Health Study. Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are associated with C-reactive protein. The common P446L polymorphi...
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[GWAS:None]
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per the 23andMe blog, the minor allele of this SNP (A) was associated with decreased LDL cholesterol, increased HDL cholesterol and increased triglycerides {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [Pharm...
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[GWAS:Triglycerides]
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[GWAS:Triglycerides]
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[GWAS:Triglycerides]
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This appears to be the snp on the Illumina Human 550 which is closest to rs4420638 [PharmGKB:Non-Curated GWAS results: Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. (Initial Sample Size: 17,815 individuals; Replication Sample Size: NR); (Region: 19q13.32; Reported Gene(s): TOMM40, APOE; Risk Allele: rs439401-G); (p-value= 0.000000002).This variant is associated with Triglycerides.] [GWAS:Triglycerides]
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[GWAS:None]
metabolic consequences
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rs780094, a SNP in the GCKR gene encoding the glucokinase regulatory protein, contributes to the risk of type-2 diabetes and dyslipidaemia in mulitple populations. The effect on type 2 diabetes is probably mediated through impaired beta cell function rather than through obesity. The rs780094(A) risk allele is associated with the following traits : * higher levels of fasting serum triacylglycerol * impaired fasting and OGTT-related insulin release * dyslipidemia * somewhat reduced risk of type-2 diabetes There may also be an additive effect between this SNP and a SNP known as 'GCK -30A', rs1799884, at least on fasting serum insulin levels. rs780094 influences severe hypertriglyceridemia. 132 patients of European ancestry with severe HTG (fasting plasma TG>10 mmol/L), and 351 matched norm...
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[GWAS:Breast size]
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The G allele of rs4846914 is associated with higher risk of hypertriglyceridemia. ] [PharmGKB:Non-Curated GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 1q42.13; Reported Gene(s): GALNT2; Risk Allele: rs4846914-G); (p-value= 0.00000004).This variant is associated with HDL cholesterol.] [GWAS:HDL cholesterol] [GWAS:Triglycerides]
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The hepatocyte growth factor receptor (MET) gene is not associated with refractive error and ocular biometrics in a Caucasian population. [GWAS:Triglycerides]
References:1
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[GWAS:Triglycerides]
lower HDL cholesterol
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The (A) allele of rs326 was associated with risk for lower high-density lipoprotein (HDL) cholesterol plasma levels in 3 independent population samples, including both Caucasians and African-Americans. [PharmGKB:Curated This SNP has been associated with small changes in HDL cholesterol levels. The A allele has been correlated with lower HDL.] [OMIM:LIPOPROTEIN LIPASE; LPL] [GWAS:Triglycerides]
Frequency: 52.2%
References:21
References:21
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rs17321515 influences severe hypertriglyceridemia. 132 patients of European ancestry with severe HTG (fasting plasma TG>10 mmol/L), and 351 matched normolipidemic controls [PharmGKB:Non-Curated GWAS Results: Newly identified loci that influence lipid concentrations and risk of coronary artery disease (Initial Sample Size: 8,684 individuals; Replication Sample Size: 5,312-9,707 individuals; Risk Allele: rs17321515-A). This variant is associated with triglyceride levels.] [GWAS:Triglycerides] [GWAS:Triglycerides]
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TRIB1 and GCKR polymorphisms, lipid levels, and risk of ischemic heart disease in the general population. Investigation of variants identified in caucasian genome-wide association studies for plasma high-density lipoprotein cholesterol and triglycerides levels in Mexican dyslipidemic study samples. [PharmGKB:Non-Curated GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 8q24.13; Reported Gene(s): TRIB1; Risk Allele: rs2954029-T); (p-value= 3E-19).This variant is associated with Triglycerides.] [GWAS:HDL cholesterol]
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[GWAS:Triglycerides]
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[GWAS:None]
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[PharmGKB:Non-Curated GWAS results: Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. (Initial Sample Size: 17,815 individuals; Replication Sample Size: NR); (Region: 1p31.3; Reported Gene(s): DOCK7; Risk Allele: rs1167998-C); (p-value= 0.000000000002).This variant is associated with Triglycerides.] [GWAS:Triglycerides]
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[GWAS:None]
Frequency: 54.0%
References:6
References:6
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per the 23andMe blog, the minor allele of this SNP (A) was associated with decreased cholesterol and triglycerides {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [PharmGKB:Non-Curated GWAS results: Loci influe...
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[GWAS:Triglycerides]
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per the 23andMe blog, the minor allele of this SNP (A) was associated with decreased LDL cholesterol, increased HDL, and decreased triglycerides {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [PharmGKB:Non-Cur...
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[GWAS:Triglycerides]
References:1
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[GWAS:Triglycerides]
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gwas among adults residing on Korcula Island in Croatia, triglycerides, the G allele associated with decreased triglyceride levels<br><br> [PharmGKB:Non-Curated GWAS results: Genome-wide association study of biochemical traits in Korcula Island, Croatia. (Initial Sample Size: 898 individuals; Replication Sample Size: NR); (Region: Xq23; Reported Gene(s): ZCCHC16; Risk Allele: rs5982533-G); (p-value= 0.000007).This variant is associated with Biochemical measures.] [GWAS:Biochemical measures]
common on affy axiom data
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[PharmGKB:Non-Curated GWAS Results: Genome-wide scan identifies variation in MLXIPL associated with plasma triglycerides (Initial Sample Size: 2,011 individuals; Replication Sample Size: 10,536 individuals; Risk Allele: rs1558861-A).] [GWAS:None] [GWAS:Triglycerides]
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The rs964184(G;G) genotype is associated with hypertriglyceridemia. [PharmGKB:Non-Curated GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 11q23.3; Reported Gene(s): APOA1, APOC3, APOA4, APOA5; Risk Allele: rs964184-G); (p-value= 0.000000000001).This variant is associated with HDL cholesterol.] [GWAS:HDL cholesterol]
29 snps
(hide) Trusight Tumor panel
1.28x increased Basal Cell Carcinoma risk. Increased risk of this kind of skin cancer. This is the most common kind of cancer in the United States. This kind has less danger of metastasizing, but still needs to be treated if it occurs. Note that if you have both the Basal Cell Carcinoma mutations, your combined risk would be 2.68x.
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2 SNPs located in different regions of chromosome 1 are likely to be associated with increased risk for basal cell carcinoma (BCC), the most common form of skin cancer. *each A at rs7538876 yields a 1.28x increased risk of developing BCC (p = 4.4 x 10e-12) *each G at rs801114 also yields a 1.28x increased odds of developing BCC (p = 5.9 x 10e-12) *2.68x increased risk of BCC for homozygous carriers of both SNPs This study was based on an analysis of ~2,000 Icelandic and Eastern European skin cancer patients (as well as a large number of controls). The authors estimate that approximately 1.6% of all individuals of European ancestry are homozygous for both risk alleles, and thus that percentage of the population is at 2.68x higher risk for BCC compared to individuals who are rs7538876(G;G) a...
Magnitude: 2
Frequency: 7.1%
Repute:Bad
References:14
Frequency: 7.1%
Repute:Bad
References:14
Possible elevated thyroid cancer risk After combining the results, three variants were shown to associate with thyroid cancer: rs966423 on 2q35 (OR = 1.34; P(combined) = 1.3 × 10(-9)), rs2439302 on 8p12 (OR = 1.36; P(combined) = 2.0 × 10(-9)) and rs116909374 on 14q13.3 (OR = 2.09; P(combined) = 4.6 × 10(-11)), a region previously reported to contain an uncorrelated variant conferring risk of thyroid cancer.
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[GWAS:None]
Normal risk of Basal Cell Carcinoma. Normal risk for this kind of skin cancer.
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2 SNPs located in different regions of chromosome 1 are likely to be associated with increased risk for basal cell carcinoma (BCC), the most common form of skin cancer. *each A at rs7538876 yields a 1.28x increased risk of developing BCC (p = 4.4 x 10e-12) *each G at rs801114 also yields a 1.28x increased odds of developing BCC (p = 5.9 x 10e-12) *2.68x increased risk of BCC for homozygous carriers of both SNPs This study was based on an analysis of ~2,000 Icelandic and Eastern European skin cancer patients (as well as a large number of controls). The authors estimate that approximately 1.6% of all individuals of European ancestry are homozygous for both risk alleles, and thus that percentage of the population is at 2.68x higher risk for BCC compared to individuals who are rs7538876(G;G) a...
Normal risk of developing bladder cancer. This is the normal risk of bladder cancer, particularly in Europeans and in people who already have tumors with low risk of progression.
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rs710521 is a SNP located in chromosome region 3q38, near the TP63 gene. A study ultimately totaling over 4,000 bladder cancer patients of European ancestry (and 40,000 controls) concluded that individuals carrying two copies of rs710521(A) were at 1.4x increased risk (allele-specific odds ratio = 1.19, p = 1 x 10e-7) for the disease. An additional 1,425 bladder cancer patients, supplemented by a meta-analysis of 5,695 additional cases (and 40,000+ controls), did replicate a (somewhat) increased risk associated with the rs710521(A) allele. The overall odds ratio was 1.18 (OR: 1.12 - 1.25, p < 0.0001). Another study in Chinese populations did not find an increased risk of bladder cancer for this SNP. [PharmGKB:Non-Curated GWAS Results: Sequence variant on 8q24 confers susceptibility to ...
1.7x higher risk of aggressive neuroblastoma
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Each G allele has been associated with an allelic odds ratio of 1.68 (p = 8.65 x 10(-18)) for risk of aggressive neuroblastoma. [OMIM:NEUROBLASTOMA]
~1.5x increased risk for chronic lymphocytic leukemia
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rs872071 is a SNP associated with the interferon regulatory factor 4 IRF4 gene. In a GWAS study including over 1,500 Caucasian patients with chronic lymphocytic leukemia (CLL), the rs872071(G) allele showed the strongest association (p = 1.91 x 10e-20) of all SNPs studied. The reported odds ratio was 1.54. See also: 23andMe blog A subsequent study () has found a similar association extending to another 800+ Spanish and Swedish CLL patients. rs872071 was also seen to be associated with CLL in Hong Kong Chinese (71 patients), with a reported odds ratio of 1.78 (CI: 1.25-2.53). A related hematologic malignancy, Hodgkin's lymphoma, may also be influenced by rs872071. Two case-control series totalling 529 and 2192 patients found an odds ratio of 1.21 (CI: 1.05-1.39, p = 0.009). [PharmGKB:Non-C...
1.3x higher risk for glioma development
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23andMe blog rs2736100 C 1.27 Glioma Lung cancer susceptibility locus at 5p15.33. Common genetic variants on 5p15.33 contribute to risk of lung adenocarcinoma in a Chinese population. Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility. Deciphering the impact of common genetic variation on lung cancer risk: a genome-wide association study. Role of 5p15.33 (TERT-CLPTM1L), 6p21.33 and 15q25.1 (CHRNA5-CHRNA3) variation and lung cancer risk in never-smokers. Individuals susceptible to lung adenocarcinoma defined by combined HLA-DQA1 and TERT genotypes. New insights into susceptibility to glioma. Replication of lung cancer susceptibility loci at chromosomes 15q25, 5p15, and 6p21: a pooled analysis from the International Lung Cancer Consortium. Evaluatio...
normal oral/throat cancer risk; more frequent alcohol consumption
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A SNP in rs1229984 encodes a form of the alcohol dehydrogenase ADH1B gene that significantly reduces the clearance rate of alcohol from the liver. This SNP is also known as Arg48His, with the (G) allele corresponding to the Arg and the (A) to the His. Known in the literature as ADH2*2 or sometimes ADH1B*2, the allele with increased activity (meaning more rapid oxidation of ethanol to acetaldehyde) is His48, encoded by rs1229984(A). Individuals with one or especially two ADH2*2 alleles, ie genotypes rs1229984(A;G) or rs1229984(A;A) are more likely to find drinking unpleasant and have a somewhat reduced risk for alcoholism. A study of over 3,800 cases of 'upper aerodigestive' cancers (mouth/throat, voice box, and esophageal cancers) concluded that the rs1229984(A) allele (in dbSNP orientatio...
Magnitude: 1.1
Frequency: 48.7%
Repute:Bad
References:40
Frequency: 48.7%
Repute:Bad
References:40
1.12x increased risk for breast cancer
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rs13387042(A;A) has an estimated 1.44-fold greater risk of breast cancer than the GG genotype. This initial association was later tested among patients in the Breast Cancer Association Consortium, including 31,510 women with invasive breast cancer, 1101 women with ductal carcinoma in situ (DCIS), and 35,969 controls. In Caucasian women of European origin, each A allele is associated with 1.12 higher odds (CI: 1.09-1.15). This association held regardless of ER or PR status. [PharmGKB:Non-Curated GWAS results: A multistage genome-wide association study in Breast Cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1). (Initial Sample Size: 1,145 cases, 1,142 controls; Replication Sample Size: 8,625 cases, 9,657 controls); (Region: 2q35; Reported Gene(s): Intergenic; Risk Alle...
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[GWAS:None]
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cancer-genetics these snps influence genetic risk for prostate cancer rs2660753 showed a per-allele OR, 1.08 (95% confidence interval, 1.00-1.16; P = 0.06) An initial report of an association with between this SNP and risk for ovarian cancer was not replicated when the same authors expanded the study over 12 studies comprising 4,482 cases (and over 6,000 controls). [GWAS:Prostate cancer]
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[GWAS:None]
References:1
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[GWAS:Prostate cancer]
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[PharmGKB:Non-Curated GWAS results: Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. (Initial Sample Size: 12,611 individuals; Replication Sample Size: 7,187 individuals); (Region: 3q23; Reported Gene(s): ZBTB38); (p-value= 0.000000000003).This variant is associated with Height.] [OMIM:STATURE QUANTITATIVE TRAIT LOCUS 10; STQTL10] [GWAS:Height] [GWAS:Height]
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[OMIM:?] [GWAS:Nasopharyngeal carcinoma]
References:1
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[GWAS:None]
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[GWAS:Prostate cancer]
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23andMe reports that rs7579899(A,A) homozygotes are 1.15 times more likely, and (G,G) homozygotes 1.15 times less likely, than (A,G) heterozygotes to develop renal cell carcinoma (a form of kidney cancer). [GWAS:None]
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rs4488809 is a SNP associated with non-small cell lung cancer (NSCLC), which comprises the vast majority of lung cancer cases. Encompassing adenocarcinoma, squamous cell carcinoma, large cell carcinoma, and other less common subtypes, NSCLC accounts for nearly all cases of lung cancer in non-smokers. NSCLC is usually treated via a combination of surgical tumor resection, chemotherapy, and radiation therapy. However, despite advances in treatment in recent years, including the development of targeted therapies against specific mutations, the prognosis for NSCLC is still bleak, and it remains the leading cause of death due to cancer worldwide. rs4488809 is located on chromosome 3q28, in the TP63 locus. This SNP was first linked to NSCLC by Miki et al. in 2010. The authors noted that while pr...
Frequency: 19.5%
References:4
References:4
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Genetic variant in TP63 on locus 3q28 is associated with risk of lung adenocarcinoma among never-smoking females in Asia. [GWAS:Lung adenocarcinoma]
Frequency: 30.1%
References:2
References:2
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[GWAS:Prostate cancer]
Frequency: 40.7%
References:4
References:4
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[GWAS:Prostate cancer]
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[GWAS:Prostate cancer]
1.7x higher risk of aggressive neuroblastoma
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23andMe blog Each copy of a G at this SNP increases the odds of aggressive neuroblastoma by 1.68 times. allelic odds ratio of 1.68 (p = 2.74 x 10(-16)) Chromosome 6p22 locus associated with clinically aggressive neuroblastoma. [OMIM:NEUROBLASTOMA] [GWAS:None]
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[GWAS:None]
References:9
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23andMe blog chronic lymphocytic leukemia *rs13397985 G 1.41 [PharmGKB:Non-Curated GWAS Results: A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia (Initial Sample Size: 505 cases, 1,438 controls; Replication Sample Size: 1,024 cases, 1,677 controls; Risk Allele: rs13397985-G). This variant is associated with Chronic lymphocytic leukemia.] [GWAS:None] [GWAS:Chronic lymphocytic leukemia]
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[GWAS:None]
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[GWAS:None]
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[GWAS:Chronic lymphocytic leukemia]
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[OMIM:?] [GWAS:Breast cancer]
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Hodgkin lymphoma [GWAS:Hodgkin's lymphoma]
None
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shows a significantly stronger association with more aggressive forms of prostate cancer (odds ratios (OR) = 1.15; P = 7.7 x 10(-9)). [PharmGKB:Curated GWAS Results: Common sequence variants on 2p15 and Xp11.22 confer susceptibility to prostate cancer (Initial Sample Size: 1,854 cases, 21,372 controls; Replication Sample Size: 8,239 cases, 7,590 controls; Risk Allele: rs721048-A).] [OMIM:EH DOMAIN-BINDING PROTEIN 1; EHBP1] [GWAS:Prostate cancer]
Frequency: 44.2%
References:2
References:2
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[GWAS:None]
Frequency: 33.0%
References:5
References:5
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23andMe blog chronic lymphocytic leukemia *rs17483466 G 1.39 Genetic susceptibility for chronic lymphocytic leukemia among Chinese in Hong Kong. [PharmGKB:Non-Curated GWAS Results: A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia (Initial Sample Size: 505 cases, 1,438 controls; Replication Sample Size: 1,024 cases, 1,677 controls; Risk Allele: rs17483466-G). This variant is associated with Chronic lymphocytic leukemia.] [GWAS:None] [GWAS:Chronic lymphocytic leukemia]
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rs20541 is a C/T polymorphism on the interleukin 13 gene IL13 associated with IgE levels. rs20541 influences the effect of maternal smoking during pregnancy and persistent childhood asthma rs1295685 and rs20541 were significantly associated with elevated IgE levels in pooled analyses. rs2569190(T;T) and rs2569191(C;C) genotypes associated with lower IgE 23andMe blog psoriasis Europeans rs20541(G) 1.27x risk [PharmGKB:Non-Curated GWAS results: Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways. (Initial Sample Size: 1,359 cases, 1,400 controls; Replication Sample Size: 5,048 cases, 5,041 controls); (Region: 5q31.1; Reported Gene(s): IL13; Risk Allele: rs20541-G); (p-value= 0.000000000000005).This variant is associated with Psoriasis.] [OMIM:PSORIASIS SUSCEP...
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Nasopharyngeal Cancer [OMIM:?] [GWAS:Nasopharyngeal Carcinoma]
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Detection, imputation, and association analysis of small deletions and null alleles on oligonucleotide arrays. [OMIM:?] [GWAS:Nasopharyngeal carcinoma]
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Detection, imputation, and association analysis of small deletions and null alleles on oligonucleotide arrays. Identification of genes with allelic imbalance on 6p associated with nasopharyngeal carcinoma in southern Chinese. [OMIM:?] [GWAS:Nasopharyngeal Carcinoma]
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[GWAS:None]
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news the presence of the G allele was protective against follicular lymphoma, while the presence of the A allele was predictive of an increased risk of developing follicular lymphoma. Dr. Brown said individuals who had the A variant were nearly twice as likely to develop follicular lymphoma. 23andMe blog coverage [OMIM:?] [GWAS:Follicular lymphoma]
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The A allele appears to protect against Hodgkin lymphoma.
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[GWAS:Hodgkin's lymphoma]
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Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX. Genome-wide association study of rheumatoid arthritis by a score test based on wavelet transformation. Multi-locus HLA class I and II allele and haplotype associations with follicular lymphoma. [GWAS:None]
References:4
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[GWAS:Follicular lymphoma]
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[GWAS:Alopecia areata]
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23andMe blog each rs210138(G) was found to increase the odds of testicular cancer by 1.5x [OMIM:?] [GWAS:Testicular germ cell tumor]
Frequency: 47.8%
References:18
References:18
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[GWAS:None]
normal
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rs401681 is a SNP in the CLPTM1-like CLPTM1 gene. The following studies span several types of cancer, and over 30,000 cases and 45,000 controls. deCODE press release reports rs401681 linked to basal cell carcinoma and many cancers for individuals with shorter telomeres, whereas those with long telomeres are at greater risk of melanoma. Neighboring rs2736098 also increases risk of cancer by affecting telomerase reverse transcriptase. The risk of these different cancers conferred by these two SNPs appears to be independent. 23andMe blog rs2736098 and rs401681 linked to many cancers, including susceptibility to pancreatic cancer However, a very large study (encompassing thousands of cases and controls) found no association between rs401681 and either (1) mean telomere length, or, (2) breast c...
Frequency: 35.4%
References:3
References:3
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[GWAS:None]
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[GWAS:None]
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rs2072590 is a SNP on chromosome 2q31, in a noncoding region ~5 kb distal to the HOXD3 gene and ~10 kb proximal to HOXD1. A genome-wide association study ultimately including over 10,000 ovarian cancer patients found statistically strong (p = 3.8 × 10e?14) evidence for slightly elevated risk associated with the rs2072590(T) allele, with an odds ratio of 1.20 (CI: 1.14–1.25) as calculated for the serous subtype (of ovarian cancer), though it was significant for the other subtypes as well. [GWAS:None]
normal
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rs889312 is a SNP near the MAP3K1 gene. rs889312 was one of the four strongest associating SNPs found in a genome-wide association study of over 4,000 breast cancer samples. . From a DeCode user report, it appears that the risk allele is C; this A;A individual reportedly has 0.93x risk of breast cancer. In a study of 1,267 breast cancer patients, rs889312 heterozygotes and minor allele homozygotes were less likely to be lymph node positive at breast cancer diagnosis (P = 0.044) relative to major allele homozygote carriers. A meta-analysis including 26,015 cases and 33,962 controls concludes that the rs889312(C) allele is clearly a significant - but quite weak - contributor to increased risk for breast cancer. breast cancer *rs2981582, rs3803662, and rs889312) showed weak but significant as...
57 snps
(hide) Variable number tandem repeat
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- rs2227902 and rs3796530 were found to be in 100% LD with a variable number tandem repeat (VNTR) length variant in the REST gene in a sample of 746 elderly Caucasians. Minor alleles (T and A, respectively) at both locations associated with the 4-length VNTR, while common alleles associated with the VNTR 5-length repeat. Carriers of the 4-length VNTR homozygous for the Val66 variant in the BDNF gene performed slightly, but significantly (p = 0.004), better than those without in the general cognitive tests performed in the study. Carriers of the 5-length VNTR and the 66Met BDNF variant had significantly lower g (p = 0.01), but the effect was not as great as the individual effect of the 66Met allele.
1 snp
(hide) Vitamin D
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Levels of 25-hydroxyvitamin D in familial longevity: the Leiden Longevity Study. Concluded that familial longevity was associated with a lower vitamin D levels and a lower frequency of the allelic variation in the CYP2R1 gene. Genome-wide association study of circulating vitamin D levels. This SNP is part of CYP2R1, which encodes a key C-25 hydroxylase that converts vitamin D3 to an active vitamin D receptor ligand. This SNP, along with rs2282679, rs3829251, and rs6599638 accounted for 2.8% of the variance in circulating vitamin D levels. [GWAS:Vitamin D levels]
Frequency: 15.0%
References:1
References:1
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Associated with periodontitis in a study of Chinese patients. rs2228570 aka rs10735810 allele (A) observed for breast cancer odds ratio (OR) of 1.26 Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity and osteoporosis. Patterns of linkage disequilibrium and haplotype distribution in disease candidate genes. Variants in the vitamin D receptor gene and asthma. Gene-environment interaction effects on the development of immune responses in the 1st year of life. Vitamin D receptor polymorphisms are associated with Graves' disease in German and Polish but not in Serbian patients. Asthma families show transmission disequilibrium of gene variants in the vitamin D metabolism and signalling pathway. Polymorphisms in the ...
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rs2238135 is a SNP in the vitamin D VDR receptor gene. rs2238135(G;G) homozygotes were associated with an ~2.5x higher risk of prostate cancer compared to homozygote carriers of the more common (C) allele in the 630 Caucasian patients studied.
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rs3847987 in the vitamin D pathway was associated with the time to onset of COPD. The SNP is a cytosine-to-adenine switch, and men with two copies of the adenine variant were more likely to develop COPD. The hazard ratio was 1.60, with a 95% confidence interval from 1.26 to 2.05, which was significant at P=0.005. news
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rs731236 protection from breast cancer (OR=0.80, 95%CI=0.64-0.99; p= 0.047) [PharmGKB:Curated This variant was significantly associated with acquired resistance to clodronate treatment in Caucasian patients with Paget's disease of the bone]
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Variants in the vitamin D receptor gene and asthma. Vitamin D receptor polymorphisms are associated with Graves' disease in German and Polish but not in Serbian patients. Asthma families show transmission disequilibrium of gene variants in the vitamin D metabolism and signalling pathway. Polymorphisms in the vitamin D receptor and their associations with risk of schizophrenia and selected anthropometric measures. Vitamin D pathway gene polymorphisms, diet, and risk of postmenopausal breast cancer: a nested case-control study. Optimization of candidate-gene SNP-genotyping by flexible oligonucleotide microarrays; analyzing variations in immune regulator genes of hay-fever samples. Vitamin D receptor gene (VDR) associations with cancer. Genome-wide association with bone mass and geometry in t...
Intermediate risk of low bone mineral density disorders
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rs1544410, also known as the BsmI polymorphism, is a SNP in the Vitamin D receptor (VDR). Multiple studies examining bone mineral density (BMD) in women have associated the A allele with increased risk of low BMD , , & . Additionally, A meta-analysis of 26 studies estimated a decreased risk of osteoporosis associated with the G;G genotype with an odds ratio of 0.61, 95% CI, 0.40-0.92 . rs1544410 increases susceptibility to Shorter stature for carriers of the A allele [PharmGKB:Curated This variant is associated with etidronate response in Caucasian (Slovenian) postmenopausal women (24 patients), with bb genotype associated with lower increase in bone mineral density (BMD) after bisphosphonate treatments.]
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rs2107301 is a SNP in the vitamin D VDR receptor gene. rs2107301(T;T) homozygotes were associated with an ~2.5x higher risk of prostate cancer compared to homozygote carriers of the more common (C) allele in the 630 Caucasian patients studied.
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[PharmGKB:In-Depth Associated with response to bronchodilators]
Frequency: 40.9%
References:2
References:2
Frequency: 33.6%
References:11
References:11
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Genome-wide association with bone mass and geometry in the Framingham Heart Study. Vitamin D receptor gene polymorphisms and epithelial ovarian cancer risk. CDX2 VDR polymorphism and colorectal cancer. Vitamin D receptor gene haplotypes and susceptibility to HIV-1 infection in injection drug users. Vitamin D receptor gene polymorphisms and haplotypes and postmenopausal breast cancer risk. Association of vitamin D receptor gene variants, adiposity and colon cancer. Modification of the inverse association between dietary vitamin D intake and colorectal cancer risk by a FokI variant supports a chemoprotective action of Vitamin D intake mediated through VDR binding. Circulating 25-hydroxyvitamin D, VDR polymorphisms, and survival in advanced non-small-cell lung cancer. Colon tumor mutations an...
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Physiogenomic comparison of human fat loss in response to diets restrictive of carbohydrate or fat. Vitamin d pathway genes, diet, and risk of renal cell carcinoma.
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A study of 414 (ex)-smokers older than 50 years concluded that vitamin D levels were reduced by 25% in rs7041](T;T) homozygotes (p<0.0001), and even after correction for age, gender and smoking history, they were also at increased risk for chronic obstructive pulmonary disease (COPD; odds ratio 2.11, CI: 1.20-3.71, p=0.009). They conclude that since vitamin D deficiency occurs frequently in COPD and correlates with its severity, vitamin D supplementation may be warranted in patients with severe COPD, and especially in those carrying rs7041(T) alleles. [OMIM:?] [GWAS:Serum vitamin D-binding protein levels]
normal Rs3135391(C;C) is highly correlated with the HLA-DRB1*1501 allele. There is no additional risk of multiple sclerosis associated with the (C;C) genotype.
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rs3135391 is highly correlated with the HLA-DRB1*1501 allele. The risk allele (T), is associated with a 3 to 6 fold higher risk for developing multiple sclerosis, and is the most significantly associated risk factor for MS. [PMC2892470] In one study, for example, the odds ratio was reported to be 3.04 (p < 1 x 10e-78). The HLA-DRB1*1501 allele has also been associated with other autoimmune diseases, such as systemic lupus erythematosis (SLE) (see) and possibly narcolepsy. The HLA-DRB1*1501 allele is fairly common; for example, it occurs in 15-30% of individuals of Northern European ancestry. [PMC2892470] An interesting series of correlations have been woven together to suggest that a possible way to lower the risk of rs3135388(T) carriers developing multiple sclerosis would be to ensure...
normal Rs3135388(C;C) is highly correlated with the HLA-DRB1*1501 allele. There is no additional risk of multiple sclerosis associated with the (C;C) genotype.
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rs3135388(T) is highly (> 99%) correlated with the HLA-DRB1*1501 allele; the risk allele (T) is associated with a 3 to 6 fold higher risk for developing multiple sclerosis. The risk per allele (or per haplotype) appears additive. It has also been associated with other autoimmune diseases, such as systemic lupus erythematosis (SLE) (see) and, when linked with DQB1*0602, narcolepsy. The HLA-DRB1*1501 allele is fairly common; for example, it occurs in 15-30% of individuals of Northern European ancestry. Note: most publications refer to the risk allele as rs3135388(A), but in dbSNP and SNPedia orientation, it is rs3135388(T). An interesting series of correlations have been woven together to suggest that a possible way to lower the risk of rs3135388(T) carriers developing multiple sclerosis ...
24 snps
(hide) Weight management
watch out for high fat in diet
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rs1801282, also known as Pro12Ala, is a common SNP in the peroxisome proliferator-activated receptor PPARG gene. The more common (C) allele (in dbSNP orientation) encodes the 'Pro' amino acid at this SNP position. rs1801282 has been reported to be associated with metabolic syndrome, but other studies have not been able to replicate any strong or significant effect. The association between type-2 diabetes and SNP rs1801282 is mentioned as being replicated in rs1801282 and risk of cognitive decline in elders? Maybe with diabetes. A ten-year study of 679 male patients with symptomatic coronary artery disease found that rs1801282(G) carriers had a much lower (10 year) cardiovascular risk, with the hazard ratio estimated to be 0.10 (CI: 0.01-0.70, p = 0.02) for ischemic heart disease and 0.24 f...
1.3x increased risk that pediatric inhaler use may make asthma worse
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rs1042713, also known as Arg16, G16R, and 16Arg>Gly, is a SNP in the adrenergic, beta-2-, surface receptor ADRB2 gene. The rs1042713(G) allele encodes the G/glycine form that is the more common one in most populations, while rs1042713(A) encodes the R/arginine residue at this position of the ADRB2 protein. A study of 1,182 young Scottish asthma patients (age, 3-22 years) concluded that rs1042713(A) alleles are significantly associated with 'exacerbations' of their condition, regardless of treatment regimens (odds ratio 1.30, CI: 1.09-1.55, p=0.003). This didn't hold true for patients using inhalers less than once per day; and it was particularly true for those receiving daily inhaled long- or short-acting beta(2)-agonist treatment (OR, 1.64, CI: 1.22-2.20, p=.001). This may therefore in...
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rs1799883 Fatty acid binding protein 2 (FABP2) Ala54Thr; The derived allele at SNP (A54T), rs1799883, in FABP2 increases strongly with latitude (p < 0.01) and may influence weight management Identification of four gene variants associated with myocardial infarction. Association of genetic variants with atherothrombotic cerebral infarction in Japanese individuals with metabolic syndrome. Association of genetic variants with chronic kidney disease in Japanese individuals with type 2 diabetes mellitus. Development of a fingerprinting panel using medically relevant polymorphisms. Soluble fibre (Plantago ovata husk) reduces plasma low-density lipoprotein (LDL) cholesterol, triglycerides, insulin, oxidised LDL and systolic blood pressure in hypercholesterolaemic patients: A randomised trial. ...
complex; see details for increased risks
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Several susceptibilities have been linked to rs1042714, a SNP in the ADRB2 gene that is also known as the Q27E SNP. The rs1042714(C) allele encodes the glutamine (Gln; 'Q'), and the rs1042714(G) allele encodes the glutamic acid (Glu; 'E'). A study of 304 patients found that the Glu27 allele led to increased risk for idiopathic venous thromboembolism; the reported odds ratio was 1.40 (CI: 1.09-1.79, p=0.006) for carriers of at least one risk allele. A study of 334 families with at least one child with autism found that increased risk associated with the rs1042714(G;G) homozygous genotype; the odds ratio reported was between 1.33-1.60 (CI: 1.07-2.58). The risk was approximately doubled among mothers who had clinical markers for pregnancy related stress. In a study of 342 patients with type-2...
4 snps
(hide) Yasko Methylation
homozygous for C677T of MTHFR = 10-20% efficiency in processing folic acid = high homocysteine, low B12 and folate levels This is the homozygous form of the C677T allele for the MTHFR gene. It is found in approximately * 15% of Hispanic Americans * 12% of Caucasian Americans * 12% of Japanese * 6% of Germans * 3% of Asians * 2% of African Americans * 1% of Sub-Saharan Africans Numerous health effects are associated with this variant. * Hyperhomocysteinemia and neurologic disorders: a review. (2014). A review. Certain genetic factors also cause elevated homocysteine levels, such as C667T substitution of the gene encoding methylenetetrahydrofolate reductase. Elevated homocysteine has been observed in several medical conditions, such as cardiovascular disorders, atherosclerosis, myocardial i...
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer ** renal cancer * cleft lip and cleft palate * coronary artery disease * dementia * depression * hyperhomocysteinemia * migraine * neural tube d...
higher risk for endometrial cancer
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rs4633 is a variant at codon 62 of the COMT gene, however, it does not change the amino acid sequence of the COMT protein. In a study of 150 (Caucasian) cases of endometrial cancer, a significant increase in rs4633(T;T) genotype was observed in patients compared to controls (OR = 2.39, CI: 1.31-4.37, p = 0.004). Furthemore, the frequency of the C-G haplotype of rs4633-rs4680 was significantly higher in controls (p < 0.0001) than in patients. This correlated with lower expression levels of the COMT protein in carriers of these alleles. pubmed 1180576 Schizophrenia Susceptibility Genetic basis for individual variations in pain perception and the development of a chronic pain condition [PharmGKB:Curated On the basis of subjects' pain responsiveness, haplotypes involving rs6269 (A/G), rs46...
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rs731236 protection from breast cancer (OR=0.80, 95%CI=0.64-0.99; p= 0.047) [PharmGKB:Curated This variant was significantly associated with acquired resistance to clodronate treatment in Caucasian patients with Paget's disease of the bone]
Intermediate risk of low bone mineral density disorders
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rs1544410, also known as the BsmI polymorphism, is a SNP in the Vitamin D receptor (VDR). Multiple studies examining bone mineral density (BMD) in women have associated the A allele with increased risk of low BMD , , & . Additionally, A meta-analysis of 26 studies estimated a decreased risk of osteoporosis associated with the G;G genotype with an odds ratio of 0.61, 95% CI, 0.40-0.92 . rs1544410 increases susceptibility to Shorter stature for carriers of the A allele [PharmGKB:Curated This variant is associated with etidronate response in Caucasian (Slovenian) postmenopausal women (24 patients), with bb genotype associated with lower increase in bone mineral density (BMD) after bisphosphonate treatments.]
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Yasko Methylation Catalyzes the hydrolysis of AdoHcy to adenosine and homocysteine. AdoHcy hydrolysis serves not only to sustain the flux of methionine sulfur toward cysteine, but is believed also to play a critical role in the regulation of biologic methylations.
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Yasko Methylation Catalyzes the hydrolysis of AdoHcy to adenosine and homocysteine. AdoHcy hydrolysis serves not only to sustain the flux of methionine sulfur toward cysteine, but is believed also to play a critical role in the regulation of biologic methylations. This is one of the SNPs reported by NutraHacker.
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Yasko Methylation Catalyzes the hydrolysis of AdoHcy to adenosine and homocysteine. AdoHcy hydrolysis serves not only to sustain the flux of methionine sulfur toward cysteine, but is believed also to play a critical role in the regulation of biologic methylations. This is one of the SNPs reported by NutraHacker.
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A and G alleles of rs4343 are strongly associated marking insertion and deletion alleles of ACE I/D respectively. For those looking for the ACE Alu Insertion/Deletion, this is a very good substitute for people searching for ACE Del16. G would mean deletion. A haplotype of rs4311, rs4343, rs699 increases risk of diabetic nephropathy 4x. [PharmGKB:Curated While the ACE:I/D has dbSNP identifiers rs1799752, rs4340, rs13447447 and rs4646994, measurement of a single base at these positions does not give an informative genotype. In Europeans, rs4343 is in complete LD with the ACE:I/D, with the A and G alleles of rs4343 marking the insertion and deletion alleles of ACE:I/D respectively.] [GWAS:Angiotensin-converting enzyme activity]
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Yasko Methylation The product the BHMT gene is central to the ‘short cut’ through the methylation cycle, again helping to convert homocysteine to methionine. The activity of this gene product can be affected by stress, by cortisol levels and may play a role in ADD/ADHD by affecting norepinephrine levels. Yasko believes that believes BHMT-02 and BHMT-04 play a role in the gut environment. Yasko also believes that BHMT-08 is related to the impact that psychological stress has on a patient's attention levels.
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No association of single nucleotide polymorphisms in one-carbon metabolism genes with prostate cancer risk. Lack of association of polymorphisms in homocysteine metabolism genes with pseudoexfoliation syndrome and glaucoma.
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pancreatic cancer 702 cases and 785 controls *rs162049 P = .0018; OR, 1.33; 95% CI: 1.11-1.60 *rs10380 (His595Tyr) P = .0063; OR, 1.45; 95% CI: 1.11-1.88
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower COMT enzymatic activity, therefore higher dopamine levels; lower pain threshold, enhanced vulnerability to stress, yet also more efficient at processing information under most conditions *rs4680(G) = Warrior. Val, less exploratory, higher COMT enzymatic activity, therefore lower dopamine levels; higher pain threshold, better stress resiliency, albeit with a modest reduction in executive cognition performance under most conditions Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis; summary at ) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compar...
normal risk
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rs1799983 (also known as Glu298Asp, E298D, or G894T) located in the NOS3 gene was associated with an ~2x risk (p=0.006) of developing pre-eclampsia (pregnancy-induced hypertension) and further complications of it in a study of ~50 African women. A large meta-analysis combining 26 studies (9,867 patients) found that homozygosity for rs1799983(T;T) increases risk of ischemic heart disease. The odds ratio was 1.31 (CI: 1.13-1.51). However, a study of 1,600 Greek patients concluded that rs1799983 was not associated with risk of acute myocardial infarction in that population. left ventricular hypertrophy in human essential hypertension OR=1.5 [PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: Women assigned to chemotherapy who had NOS3 −786 CC and 894 TT genotypes had a...
normal
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rs1801394, also known as A66G or Ile22Met, is a SNP in the methionine synthase MTRR gene. This gene encodes one of the two enzymes involved in the production of methionine (the other is MTR). The protein encoded by an rs1801394 allele has a lower affinity for MTR () and is inconsistently associated with homocysteine level, although it is a risk factor for neural tube defects () and Down syndrome () in conditions of higher homocysteine. Based on a study of British patients with primary brain tumors, (1,005 glioma cases and 631 meningioma cases), rs1801394(G;G) individuals were at higher risk for meningioma (odds ratio 1.41, CI: 1.02-1.94). In general, genotypes associated with increased 5,10-methylenetetrahydrofolate levels are associated with elevated risk for these types of brain cancer. ...
16 snps