Promethease Report

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 ...

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...

rs1800796 IL-6 572G>C polymorphism (and h.211 haplotype) is associated with abdominal aortic aneurysm (AAA). The risk allele is C. Our results provide evidence that there is a clear genetic influence of IL6 -572C>G polymorphism on plasma levels of fibrinogen and CRP, but this polymorphism does not lead to elevated blood pressure. 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 ...

Influences ABO blood group ABO Blood Type [OMIM:?]

may influence ABO blood group see gs129 ABO Blood Type

This SNP is in the ABO gene, and is therefore potentially useful in determing blood group type, such as through the use of genosets. This particular SNP can be useful in determining whether an ABO type A allele is more specifically an A1 type allele or an A2 type allele. The more common allele (80% of A types on average) is A1, consistent with having a rs55964869(C) allele, with the rarer A2 allele encoded by rs55964869(T). However, the key defining characteristic between an A1 and an A2 allele is the presence or absence of a deletion based on SNP rs8176750.

This SNP is in the ABO gene, and is therefore potentially useful in determing blood group type, such as through the use of genosets. ABO Blood Type [OMIM:?]

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 , and 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 cessation success, or finding no such association. A meta-analys...

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 (r²=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...

rs1799732 is a SNP in the D2 dopamine receptor gene DRD2 gene. Although dbSNP indicates the alleles as (C) or (-) (i.e. a deletion), investigators report the alleles as (C) or (T). In a study of individuals in the Polyp Prevention Trial with any, multiple (>/=2) or advanced colorectal adenoma recurrence after 4 years, compared to those without adenoma recurrence, rs1799732(C;T) individuals were significantly associated with all adenoma recurrence (odds ratio 1.30, CI: 1.01-1.69). The authors speculate this increased risk of adenoma recurrence (and an association with colorectal cancer) may be related to SNP-associated differences in alcohol and fat intake. 23andMe blog Alcoholism related *rs1799971(A;A) severe alcoholism 2x *rs1799732(I;I) severe alcoholism 1.85x [PharmGKB:Curated Risk...

[PharmGKB:Curated This promoter variant affects total DRD2 mRNA expression. The C allele is associated with enhanced total DRD2 mRNA expression and is associated with working memory activity in prefrontal cortex and striatum of schizophrenia patients.]

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...

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.]

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...

G allele is associated with 4.12mg/dl increase in HDL cholesterol (good cholesterol). [GWAS:HDL cholesterol]

Evaluation of new and established age-related macular degeneration susceptibility genes in the Women's Health Initiative Sight Exam (WHI-SE) Study. [GWAS:Age-related macular degeneration]

rs3732378 VAL249ILE is tightly linked to neighboring rs3732379 THR280MET The protein receptor with both variant amino acids is known as CX3CR1-M280. the minor alleles of this pair are associated with *more rapid progression to full-blown AIDS and probably increased susceptibility to HIV infection *reduced risk of acute coronary events *increased risk of age related macular degeneration [OMIM:?]

Located close to ApoE4, yet independently (also) influences risk of Alzheimer's disease. A case-control study of 381 patients found a 2x higher risk for Alzheimer's disease associated with the rarer rs2075650(G) allele. This allele is associated with earlier onset of Alzheimer's disease, by ~7 years. (news) The data from this study are available online at The association of this SNP with late-onset Alzheimer's disease] was confirmed by a study reported in PLoS Genetics. The A allele of this SNP is one of 150 identified as relevant to exceptional longevity in rs2075650 was found to be associated with Alzheimer's disease based on a study by the eMERGE network in which electronic medical records were searched to find clinical associations associated with selected SNPs. [PharmGKB:Curated GWAS...

[GWAS:Age-related macular degeneration]

age related macular degeneration [OMIM:COMPLEMENT FACTOR B; CFB] [GWAS:Age-related macular degeneration]

[GWAS:Age-related macular degeneration]

association with age-related macular degeneration (ARMD) risk allele said to be (A), in dbSNP orientation (ref: Navigenics apparently uses rs522162] as a proxy (substitute) for rs641153 [GWAS:Age-related macular degeneration]

rs547154 significantly associated with Age-related maculopathy in both our case-control (P-value 0.00007) and family data (P-value 0.00001). [OMIM:COMPLEMENT COMPONENT 2 DEFICIENCY]

[GWAS:Age-related macular degeneration]

[GWAS:Age-related macular degeneration]

rs1047286 is a SNP in the complement component C3 gene. A 2011 meta-analysis of seven studies concluded that, at least for Caucasians, the rs1047286(C;T) and (T;T) genotypes had 1.27 (CI: 1.15 - 1.41) and 1.70 (CI: 1.27 - 2.11) times higher risk of ARMD than did (G;G) genotypes. [OMIM:C3 POLYMORPHISM, HAV 4-1 PLUS/MINUS TYPE]

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]

age related macular degeneration [OMIM:COMPLEMENT FACTOR B; CFB]

age related macular degeneration Genetic markers and biomarkers for age-related macular degeneration. C2 and CFB genes in age-related maculopathy and joint action with CFH and LOC387715 genes. Analysis of rare variants in the complement component 2 (C2) and factor B (BF) genes refine association for age-related macular degeneration (AMD). Variations in five genes and the severity of age-related macular degeneration: results from the Muenster aging and retina study. Multilocus analysis of age-related macular degeneration. Plasma complement components and activation fragments: associations with age-related macular degeneration genotypes and phenotypes. Complement component 3: an assessment of association with AMD and analysis of gene-gene and gene-environment interactions in a Northern Irish...

Compared with individuals without CCR5-Delta32 (a variation in another gene) or rs1799864(A), individuals with one or two copies of rs1799864(A) had a 58% lower risk of developing AIDS during the first 4 years after testing positive for HIV, a 19% lower risk during the subsequent 4 years, and no significant protection thereafter. No protective effect (ie no benefit) was seen for this SNP once AIDS had developed. rs1799864(G), rs3025058(A) and rs662 were associated with increased risk, and rs1800775(A) with reduced risk of recurrent venous thromboembolism [OMIM:HUMAN IMMUNODEFICIENCY VIRUS TYPE 1, RESISTANCE TO]

shows that the following four SNPs in the MHC region play a particular important role in the protection of developing AIDS: rs9264942, rs4418214, rs2395029, rs3131018 also including the two variants in CCR5 rs333 (delta32) and C927T.

[GWAS:AIDS]

rs2395029 is a SNP in the major histocompatibility complex (MHC) region, and several studies have shown that the rs2395029(G) allele is 99.9% predictive of the presence of an HLA-B*5701 allele. This HLA allele, in turn, has been associated with several conditions. A study of 51 cases of flucloxacillin drug-induced liver injury (DILI), an important cause of serious liver disease, along with a replication study of another 23 cases, found that the rs2395029(G) carriers were at highly increased risk (odds ratio 80, p=8.7x10(-33)). * see also: 23andMe blog rs2395029(G;G) increases the odds of drug-induced liver injury in response to flucloxacillin by 45x This SNP is thought to be involved in determining the HIV viral load set point during the asymptomatic period of infection. This SNP is estima...

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 , and 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 cessation success, or finding no such association. A meta-analys...

rs671 is a classic SNP, well known in a sense through the phenomena known as the 'alcohol flush', also known as the 'Asian Flush' or 'Asian blush', in which certain individuals, often of Asian descent, have their face, neck and sometimes shoulders turn red after drinking alcohol. The rs671(A) allele of the ALDH2 gene is the culprit, in that it encodes a form of the aldehyde dehydrogenase 2 protein that is defective at metabolizing alcohol. This allele is known as the ALDH*2 form, and individuals possessing either one or two copies of it show alcohol-related sensitivity responses including facial flushing, and severe hangovers (and hence they are usually not regular drinkers). Perhaps not surprisingly they appear to suffer less from alcoholism and alcohol-related liver disease. Disulfiram (...

rs27072, a SNP in the dopamine transporter SLC6A3 gene, has been associated with more severe symptoms upon alcohol withdrawal, such as seizures, in a study of 250 Caucasian alcohol-dependent patients. Two haplotypes appear to be tagged by this SNP and a neighbor, rs27048. The rs27072 polymorphism has been shown to be significantly associated with ADHD in clinical samples of Canadian children aged 6 to 16 [Feng et al., 2005] and the significant association was also reported by Ouellet-Morin et al. in a Canadian twin study, 2008 (Am. J. of Medical Genetics Part B, 147B:1442-1449 (2008). The interaction between the dopamine transporter gene and age at onset in relation to tobacco and alcohol use among 19-year-olds. Association of promoter variants of human dopamine transporter gene with schiz...

The rs1799971(G) allele in exon 1 of the mu opioid receptor OPRM1 gene causes the normal amino acid at residue 40, asparagine (Asn), to be replaced by aspartic acid (Asp). In the literature this SNP is also known as A118G, N40D, or Asn40Asp. Carriers of at least one rs1799971(G) allele appear to have stronger cravings for alcohol than carriers of two rs1799971(A) alleles, and are thus hypothesized to be more at higher risk for alcoholism. However, subsequent research results are mixed, and there are other studies both agreeing or disagreeing with this finding Among 200+ alcoholics treated with naltrexone, rs1799971(G) carriers receiving the drug (even without behavioral intervention) had an increased percentage of days abstinent (p = .07) and a decreased percentage of heavy drinking days (...

rs13297480(G) a specific high-risk haplotype (p = 0.006, maximum statistic p = 0.051) for alcoholism

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 gene as well as ha...

[PharmGKB:Curated In a family linkage study, rs846664 was shown to be significantly associated with risk for alcohol dependence. The risk allele appears at a much higher frequency in African Americans than in European Americans.] [OMIM:TASTE RECEPTOR, TYPE 2, MEMBER 16; TAS2R16]

This SNP in the tumor necrosis factor-alpha gene, rs1800629, is also known as the TNF-308 SNP. Occasionally the rs1800629(A) allele is referred to as 308.2 or TNF2, with the more common (G) allele being 308.1 or TNF1. The (A) allele is associated with higher levels of TNF expression. This SNP has been linked to a wide variety of conditions: * Allograft rejection ** Among 72 Polish patients receiving a kidney transplant, the risk of acute kidney allograft rejection was 2.5x higher among rs1800629(A) carriers compared to (G;G) homozygotes (CI: 1.19- 5.37, p<.05). * Asthma ** A meta-analysis of ~2,500 patients combined indicated that the rs1800629(A) allele was associated with a 1.46x increased risk for asthma. ** In a study of ~600 Mexican families and their asthmatic children, rs1800629(...

rs4986790, a SNP also known as Asp299Gly (and also 896A/G) in the TLR4 gene, is often studied along with a cosegregating SNP known as Thr399Ile, rs4986791. (TLR4 encodes a receptor involved in the innate immune response.) Together, these SNPs have been reported to be associated with a wide variety of both infectious and non-infectious diseases, although there are conflicting or even contradictory results also reported in some cases. The risk allele for rs4986790 is (G). Reported associations include : * Diabetic neuropathy ** These SNPs may be protective * Heart disease ** Men with the risk alleles for both SNPs are at increased risk for myocardial infarction in this study of over 2000 individuals. ** rs4986790(G) carriers are not at increased risk for myocardial infartions, at least in th...

rs4986791, a SNP also known as Thr399Ile (and also 1196C/T) in the TLR4 gene, is often studied along with a cosegregating SNP known as Asp299Gly, rs4986790. (TLR4 encodes a receptor involved in the innate immune response.) Together, these SNPs have been reported to be associated with a wide variety of both infectious and non-infectious diseases, although there are conflicting or even contradictory results also reported in some cases. The risk allele for rs4986791 is (T). Reported associations include : * Diabetic neuropathy ** These SNPs may be protective * Heart disease ** Men with the risk alleles for both SNPs are at increased risk for myocardial infarction in this study of over 2000 individuals. ** rs4986790(G) carriers are not at increased risk for myocardial infartions, at least in t...

rs1143634, also known as +3954, is a SNP in the IL-1 beta IL1B gene. A study of 556 adults in the Western Australian coronary heart disease (CHD) population concluded that rs1143634(T;T) homozygotes had larger waist circumference, by 1.8cm on average, compared to major allele (C;C) homozygotes. This association was even more pronounced in patients with higher levels of obesity or inflammatory markers. rs1143634 increases susceptibility to Alopecia Areata 2.67 times for heterozygotes (CT) and 1.13 times for homozygotes (TT) rs1143634 increases susceptibility to Alzheimer's disease 2.33 times for homozygotes (TT) rs1143634 increases susceptibility to Cervical lesions, low-grade squamous intraepithelial lesions 4.29 times for heterozygotes (CT) and 3.57 times for homozygotes (TT) rs1143634 in...

rs28929474, also known as Glu342Lys as well as E366K, is a SNP in the serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1 SERPINA1 gene. This SNP is the one most frequently leading, when homozygous, to the complications of alpha-1 antitrypsin deficiency and the associated high risk of emphysema and liver disease. Between 1 - 2% of US Caucasians are thought to be (heterozygous) carriers for this SNP, leading some associations, like the Alpha-1 Foundation, to call for mass carrier screening. * 23andMe blog rs28929474(T) increases odds of liver disease in cystic fibrosis patients by 4.17 times. (T;T) at both copies of this SNP causes alpha-1 antitrypsin deficiency; note use of opposite strand nomenclature by this company. finds no association between rs28929474...

This SNP 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 allele: G Phenotype: CETP V405 valine homozygosity (GG genoty...

rs3851179 is a SNP upstream of the PICALM gene. A study of over 5,000 Alzheimer's disease patients (and over 10,000 controls) found a slight protective effect of the (A) allele of this SNP. rs3851179(A) carriers had a slightly decreased risk for Alzheimer's disease, with an odds ratio of 0.85 (CI: 0.8-0.9, p=1.9x10e-8). The association of this SNP and late-onset Alzheimer's disease was replicated over a total of another 1829 cases (and 2576 controls). [GWAS:Alzheimer's disease]

(G;G) showed a 1.9-fold increased risk of Alzheimer's disease (95 % CI 1.16-3.10, p = 0.003)

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'.

rs669 is a SNP in the alpha-2-macroglobulin A2M gene. In dbSNP orientation, the rs669(A) allele encodes an isoleucine, and the rs669(G) allele encodes a valine; the SNP is also known as the Ile/Val variant. On its own, rs669 was not seen to reproducibly and independently increase risk for Alzheimer's disease in several studies of ~200 Italian patients. However, the T-C-A haplotype of rs12316150-rs1050283-rs669 was associated with both early- and late-onset Alzheimer's disease. The majority of the disease risk from this haplotype was based on rs1050283. The original 2004 study of 148 Italian sporadic AD patients yielded an odds ratio for the rs669(G;G) genotype (as oriented in dbSNP orientation) of 3.81 (CI: 1.66-8.75). The presence of rs2333227(C;C), in addition to rs669(G;G), appears to s...

rs10519262, a intergenic SNP on chromosome 15, is reported to influence the risk for Alzheimer's disease based on a study of ~1100 Canadian patients. The risk allele is (A); the odds ratio is 1.89 (CI: 1.46 - 2.45).

While the ApoE4 allele (rs429358(C)) is widely accepted as the predominant genetic risk factor for Alzheimer's disease, there are likely to be numerous other factors, both genetic and environmental, associated to lesser degrees with susceptibility to the disease. Genes influencing the immune system, and in particular susceptibility to viral infections such as herpes, may be among such factors. This SNP, located in the TAP2 gene and thus implicated in the activation of HIV and HSV-1 viruses, is seen more commonly in ~300 Alzheimer patients than in the same number of controls. The risk allele is rs241448(C). The odds ratio is reported to be 2.14 (CI: 1.02-2.55) for rsrs241448(C;C) homozygotes, and 1.51 (CI: 0.80-1.93) for rsrs241448(C;T) heterozygotes, compared with rsrs241448(T;T) homozygot...

Nominally significant association found for this SNP with late-onset Alzheimer's disease (odds ratio 1.18, p=0.024) in a study of ~1000 Caucasian patients, but it would not have withstood statistical correction for multiple testing.

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...

[GWAS:Alzheimer's Disease]

Located close to ApoE4, yet independently (also) influences risk of Alzheimer's disease. A case-control study of 381 patients found a 2x higher risk for Alzheimer's disease associated with the rarer rs2075650(G) allele. This allele is associated with earlier onset of Alzheimer's disease, by ~7 years. (news) The data from this study are available online at The association of this SNP with late-onset Alzheimer's disease] was confirmed by a study reported in PLoS Genetics. The A allele of this SNP is one of 150 identified as relevant to exceptional longevity in rs2075650 was found to be associated with Alzheimer's disease based on a study by the eMERGE network in which electronic medical records were searched to find clinical associations associated with selected SNPs. [PharmGKB:Curated GWAS...

rs6583817, also known as v311, is a SNP within an intron of the IDE gene, which encodes the insulin-degrading enzyme. Late onset Alzheimer's disease is a neurodegenerative condition in which the brain develops large numbers of extracellular senile plaques composed primarily of aggregated amyloid-B proteins as well as intraneuronal neurofibrillary tangles composed mainly of aggregated tau protein. One notable function of insulin-degrading enzyme is its ability to degrade amyloid-B and therefore to influence the amount of amyloid-B found in the brain. A study of ~3,000 patients (and an equal number of matched controls) found that carriers of one or two minor alleles, i.e. rs6583817(T), had ~2x higher levels of insulin-degrading enzyme (p < 10e-8), lower levels of amyloid-B, and a (slightl...

rs7910977 is a SNP of the IDE gene, which encodes the insulin-degrading enzyme. Late onset Alzheimer's disease is a neurodegenerative condition in which the brain develops large numbers of extracellular senile plaques composed primarily of aggregated amyloid-B proteins as well as intraneuronal neurofibrillary tangles composed mainly of aggregated tau protein. One notable function of insulin-degrading enzyme is its ability to degrade amyloid-B and therefore to influence the amount of amyloid-B found in the brain. The rs7910977(T) allele is associated with reduced risk of Alzheimer's disease in one study of ~3,000 patients, and in this study, the conclusion was that it was most likely due to near perfect linkage with rs6583817, a nearby functional variant. rs6583817(T) allele carriers had an...

news Alzheimer's disease [PharmGKB:Curated GWAS results: Genome-wide association study implicates a chromosome 12 risk locus for late-onset Alzheimer disease. (Initial Sample Size: 492 cases, 496 controls; Replication Sample Size: 238 cases, 220 controls); (Region: 12q13.11; Reported Gene(s): FAM113B; Risk Allele: rs11610206-?); (p-value= 0.0000003).This variant is associated with Alzheimer's disease.] [GWAS:Alzheimer's disease]

rs911541 increases susceptibility to late-onset Alzheimer's disease 1.58 times for heterozygotes (A;G) and 1.48 times for homozygotes (G;G,) based on a case-control study of ~1,500 Japanese patients and an equal number of matched controls.

Alzheimer's disease associated, based on large 2011 study 'The minor allele of Rs3764650 in ABCA7 was associated with a later age at onset and shorter disease course' according to http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511432/ [GWAS:None]

Nominally significant association found for this SNP with late-onset Alzheimer's disease (odds ratio 0.79, p=0.022) in a study of ~1000 Caucasian patients, but it would not have withstood statistical correction for multiple testing.

rs3758505, rs4646953 and rs4646954 influence Alzheimer's disease

rs4986790, a SNP also known as Asp299Gly (and also 896A/G) in the TLR4 gene, is often studied along with a cosegregating SNP known as Thr399Ile, rs4986791. (TLR4 encodes a receptor involved in the innate immune response.) Together, these SNPs have been reported to be associated with a wide variety of both infectious and non-infectious diseases, although there are conflicting or even contradictory results also reported in some cases. The risk allele for rs4986790 is (G). Reported associations include : * Diabetic neuropathy ** These SNPs may be protective * Heart disease ** Men with the risk alleles for both SNPs are at increased risk for myocardial infarction in this study of over 2000 individuals. ** rs4986790(G) carriers are not at increased risk for myocardial infartions, at least in th...

This SNP is in the anterior pharynx defective 1 homolog B APH1B gene; the (T) allele encodes the Phe, while the (G) allele encodes the rarer Leu; this SNP is also known as Phe217Leu. rs1047552 previously linked to Alzheimer's disease. Analysis of a Dutch Caucasian cohort (780 cases; 1414 controls) showed a higher prevalence of the risk allele rs1047552(G) in males (OR = 1.63; p = 0.033) for coronary atherosclerosis but not females.

This SNP, located in the fourth exon of the ApoE gene, affects the amino acid at position 130 of the resulting protein. The more common rs429358 allele is (T). If the allele is (C) and the same chromosome also harbors the rs7412(C) allele, the combination is known as an Apo-ε4 allele. The Apo-ε4 allele has a strong influence on the risk of Alzheimer's disease. Both deCODEme and 23andMe (v3 chip) test for this SNP. Many studies have estimated the level of risk, and it varies depending on age, sex, ethnicity, and other factors. One meta-analysis estimated the odds ratios for homozygous rs429358(C;C) individuals compared to the more common ApoE3/ApoE3 homozygotes to be 12x for late-onset Alzheimer's and 61x for early-onset disease. Meta-analyses have also supported the association between the...

rs3758505, rs4646953 and rs4646954 influence Alzheimer's disease

The ancestral allele is C. The rs7412(T) allele, also known as Arg176Cys, generally indicates the presence of an Apoε2 allele; see the ApoE page for a full discussion of the ApoE alleles and their association with Alzheimer's disease. Another SNP related to ApoE is rs429358. In a study of 67 mostly Caucasian patients prescribed the atypical antipsychotic olanzapine, carriers of a rs7412(C) allele were more likely to gain significant weight compared to rs7412(T;T) carriers, as assessed by physiogenomic analysis of corresponding weight profiles. Two other SNPs, rs5092 and rs4765623, were also significantly associated with weight profiles in these patients. Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity and o...

Presenile dementia and cerebral haemorrhage linked to a mutation at codon 692 of the beta-amyloid precursor protein gene. Presenile Alzheimer dementia characterized by amyloid angiopathy and large amyloid core type senile plaques in the APP 692Ala-->Gly mutation. Flemish and Dutch mutations in amyloid beta precursor protein have different effects on amyloid beta secretion. Presentation of amyloidosis in carriers of the codon 692 mutation in the amyloid precursor protein gene (APP692). In vitro studies of amyloid beta-protein fibril assembly and toxicity provide clues to the aetiology of Flemish variant (Ala692-->Gly) Alzheimer's disease. [OMIM:?]

rs3825776, a SNP in the region of the LIPC gene on chromosome 15, has been associated with the sporadic form of ALS (Lou Gehrig's disease) in a study of 1000+ European patients. The odds ratio for the risk allele rs3825776(G) is 1.34 (CI: 1.12 - 1.46).

This SNP was associated with amyotrophic lateral sclerosis (ALS) based on a study of 1,152 patients.

[GWAS:Amyotrophic lateral sclerosis]

Associated with risk of amyotrophic lateral sclerosis (ALS) in two European populations [OMIM:GRANULIN PRECURSOR; GRN]

[GWAS:Amyotrophic lateral sclerosis]

[GWAS:Amyotrophic lateral sclerosis]

[GWAS:Amyotrophic lateral sclerosis]

[OMIM:?]

rs6539137 is one of several TXNRD1 SNPs significantly associated with familial amyotrophic lateral sclerosis (FALS) but not sporadic amyotrophic lateral sclerosis (ALS). The risk allele, rs6539137(A), is also associated with an earlier age of onset by 8 years, and the shift was more significant in males (in fact, insignificant in females).

rs4630362 is one of several TXNRD1 SNPs significantly associated with familial amyotrophic lateral sclerosis (FALS) but not sporadic amyotrophic lateral sclerosis (ALS).

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 ...

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 [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: 2q33.1; Reported Gene(s): BOLL, PLCL1; Risk Allele: rs700651-G); (p-value= 0.00000004).This variant is associated with Intracranial aneurysm.] [OMIM:ANEURYSM, INTRACRANIAL BERRY, 9] [GWAS:Intracranial aneurysm]

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...

Each A allele at rs2303138 in the LNPEP gene is associated with 1.5x higher odds of ankylosing spondylitis, according to a 2007 report.

rs11209032 is one of several SNPs in the IL23R gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 1.3 (p=7.5x10e-9). rs11209032 and rs1495965 no significant association with systemic sclerosis [OMIM:?]

According to a 2007 report, each G allele at rs7302230 in the CLSTN3 gene is associated with 1.6x higher odds of ankylosing spondylitis.

23andMe reports that each G allele at rs868213 appears to be associated with 1.5x higher odds of ankylosing spondylitis.

rs11465804 is one of several SNPs in the IL23R gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 0.68 (p=0.0002). [PharmGKB:Non-Curated GWAS results: Genome-wide association study for Crohn's disease in the Quebec Founder Population identifies multiple validated disease loci (Initial Sample Size: 382 trios; Replication Sample Size: 521 trios, 750 cases, 828 controls). This variant is associated with Crohn's disease. This variant is associated with Crohn's disease.] [GWAS:Crohn's disease] [GWAS:Crohn's disease]