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rs3087243

From SNPedia

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Geno Mag Summary
(A;A) 1.5 increased risk for auto-immune diseases
(A;G) 1.5 increased risk for auto-immune diseases
(G;G) 1 Normal risk for autoimmune diseases
ReferenceGRCh38 38.1/141
Chromosome2
Position203874196
GeneCTLA4
is asnp
is mentioned by
dbSNPrs3087243
ebirs3087243
HLIrs3087243
Exacrs3087243
Varsomers3087243
Maprs3087243
PheGenIrs3087243
hapmaprs3087243
1000 genomesrs3087243
hgdprs3087243
ensemblrs3087243
gopubmedrs3087243
geneviewrs3087243
scholarrs3087243
googlers3087243
pharmgkbrs3087243
gwascentralrs3087243
openSNPrs3087243
23andMers3087243
23andMe allrs3087243
SNP Nexus

SNPshotrs3087243
SNPdbers3087243
MSV3drs3087243
GWAS Ctlgrs3087243
GMAF0.3242
Max Magnitude1.5
? (A;A) (A;G) (G;G) 28
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.

[PMID 16352685] 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 arthritis (RA). A study of 2,000+ European RA patients led to a calculated odds ratio of 1.13 (CI: 1.03 - 1.24) for the rs3087243(G) risk allele. [PMID 16380915OA-icon.png]

In a study of 395 Spanish patients with lupus, rs3087243(G) allele carriers were calculated to have an odds ratio of 1.71 (CI: 1.18-2.49, p=0.003, p(corr) = 0.006).[PMID 15248219]

In a different study involving recipients of liver transplants, although also with Spanish patients, the rs3087243(G) allele was significantly associated with acute rejection (odds ratio 1.49, p(corr)=0.038). Patients who lacked this allele had the lowest risk of acute rejection development. Allograft survival data did not show statistical differences between genotypes.[PMID 18047932]

[PMID 18940880] rs2292399 and rs2903692 both significantly associated with type 1 diabetes odds ratio 1.37 and 1.28. A joint analysis revealed that rs3087243, rs2292399, and rs2903692, but not INS rs689, were significant risk factors for the cooccurrence of AITD


[PMID 19300490OA-icon.png] An African Ancestry-Specific Allele of CTLA4 Confers Protection against Rheumatoid Arthritis in African Americans.

GWAS snp
PMID [PMID 18978792OA-icon.png]
Trait Type 1 diabetes
Title Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci
Risk Allele A
P-val 8E-11
Odds Ratio NR NR
GWAS snp
PMID [PMID 19430480OA-icon.png]
Trait Type 1 diabetes
Title Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes
Risk Allele
P-val 1E-15
Odds Ratio NR NR

[PMID 19506323] The Onset of Diabetes in Three out of Four Sisters: A Japanese Family with Type 1 Diabetes. A Case Report


[PMID 19404967] Confirmation of STAT4, IL2/IL21, and CTLA4 polymorphisms in rheumatoid arthritis

OMIM123890
DescCYTOTOXIC T LYMPHOCYTE-ASSOCIATED 4; CTLA4
Variant
Relatedalso

[PMID 19895365] Functional polymorphism in CTLA4 gene influences the response to therapy with inhaled corticosteroids in Slovenian children with atopic asthma



[PMID 19951419OA-icon.png] Confirmation of the genetic association of CTLA4 and PTPN22 with ANCA-associated vasculitis


[PMID 20537165OA-icon.png] The CTLA4 variants may interact with the IL23R- and NOD2-conferred risk in development of Crohn's disease

GWAS snp
PMID [PMID 20453842OA-icon.png]
Trait Rheumatoid arthritis
Title Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk lock
Risk Allele G
P-val 1E-8
Odds Ratio 1.15 [1.10-1.20]

[PMID 20498205OA-icon.png] Investigation of potential non-HLA rheumatoid arthritis susceptibility loci in a European cohort increases the evidence for nine markers

[PMID 20825955] Clinical and genetic characteristics of patients with autoimmune thyroid disease with anti-islet autoimmunity

OMIM123890
Desc
Variant0002
Relatedalso
[PMID 21637411OA-icon.png] CTLA4CT60 gene polymorphism is not associated with differential susceptibility to pemphigus foliaceus


[PMID 21040781] CTLA-4 confers a risk of recurrent schizophrenia, major depressive disorder and bipolar disorder in the Chinese Han population

GWAS snp
PMID [PMID 21829393OA-icon.png]
Trait
Title Genome-wide association analysis of autoantibody positivity in type 1 diabetes cases.
Risk Allele A
P-val 2E-17
Odds Ratio 1.2000 [NR]


[PMID 15452244OA-icon.png] Cytotoxic T-lymphocyte antigen 4 gene and recovery from hepatitis B virus infection.


[PMID 17209142] Interaction analysis of the CBLB and CTLA4 genes in type 1 diabetes.


[PMID 17334650OA-icon.png] A type 1 diabetes subgroup with a female bias is characterised by failure in tolerance to thyroid peroxidase at an early age and a strong association with the cytotoxic T-lymphocyte-associated antigen-4 gene.


[PMID 17554260OA-icon.png] Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes.


[PMID 17606874OA-icon.png] Association of the vitamin D metabolism gene CYP27B1 with type 1 diabetes.


[PMID 17666451OA-icon.png] Associations between human leukocyte antigen, PTPN22, CTLA4 genotypes and rheumatoid arthritis phenotypes of autoantibody status, age at diagnosis and erosions in a large cohort study.


[PMID 17825114OA-icon.png] Association of CTLA-4 gene polymorphisms with sporadic breast cancer in Chinese Han population.


[PMID 17940599OA-icon.png] Assembly of inflammation-related genes for pathway-focused genetic analysis.


[PMID 18000051OA-icon.png] Allelic variant in CTLA4 alters T cell phosphorylation patterns.


[PMID 18200060] PTPN22 is genetically associated with risk of generalized vitiligo, but CTLA4 is not.


[PMID 18252225OA-icon.png] On the use of general control samples for genome-wide association studies: genetic matching highlights causal variants.


[PMID 18456185OA-icon.png] Genetics and genomics of primary biliary cirrhosis.


[PMID 18462498OA-icon.png] Genetic polymorphisms in PTPN22, PADI-4, and CTLA-4 and risk for rheumatoid arthritis in two longitudinal cohort studies: evidence of gene-environment interactions with heavy cigarette smoking.


[PMID 18466531OA-icon.png] Case-control association analysis of rheumatoid arthritis with candidate genes using related cases.


[PMID 18528295OA-icon.png] Influence of cytotoxic T lymphocyte-associated antigen 4 (CTLA4) common polymorphisms on outcome in treatment of melanoma patients with CTLA-4 blockade.


[PMID 18556337OA-icon.png] 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).


[PMID 18576317OA-icon.png] Lack of association of functional CTLA4 polymorphisms with juvenile idiopathic arthritis.


[PMID 18773895OA-icon.png] The genetic basis of primary biliary cirrhosis: premises, not promises.


[PMID 18776148OA-icon.png] Joint genetic susceptibility to type 1 diabetes and autoimmune thyroiditis: from epidemiology to mechanisms.


[PMID 18778710OA-icon.png] Primary biliary cirrhosis is associated with a genetic variant in the 3' flanking region of the CTLA4 gene.


[PMID 18794853OA-icon.png] Common variants at CD40 and other loci confer risk of rheumatoid arthritis.


[PMID 18805939OA-icon.png] Functional genetic polymorphisms and female reproductive disorders: part II--endometriosis.


[PMID 18853133OA-icon.png] Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes.


[PMID 19014504OA-icon.png] Lack of association between sCTLA-4 levels in human plasma and common CTLA-4 polymorphisms.


[PMID 19073967OA-icon.png] Shared and distinct genetic variants in type 1 diabetes and celiac disease.


[PMID 19141582OA-icon.png] Autoimmune thyroiditis and diabetes: dissecting the joint genetic susceptibility in a large cohort of multiplex families.


[PMID 19147066OA-icon.png] Genomic and proteomic analysis of allogeneic hematopoietic cell transplant outcome. Seeking greater understanding the pathogenesis of GVHD and mortality.


[PMID 19175525OA-icon.png] CTLA4 and generalized vitiligo: two genetic association studies and a meta-analysis of published data.


[PMID 19359276OA-icon.png] Identification of AF4/FMR2 family, member 3 (AFF3) as a novel rheumatoid arthritis susceptibility locus and confirmation of two further pan-autoimmune susceptibility genes.


[PMID 19609446OA-icon.png] CTLA4 autoimmunity-associated genotype contributes to severe pulmonary tuberculosis in an African population.


[PMID 19622768OA-icon.png] CTLA4 variants, UV-induced tolerance, and risk of non-melanoma skin cancer.


[PMID 19672595OA-icon.png] Polymorphisms in the CD28/CTLA4/ICOS genes: role in malignant melanoma susceptibility and prognosis?


[PMID 19740340OA-icon.png] The CTLA-4 gene polymorphisms are associated with CTLA-4 protein expression levels in multiple sclerosis patients and with susceptibility to disease.


[PMID 19956097OA-icon.png] Remapping the type I diabetes association of the CTLA4 locus.


[PMID 19956101OA-icon.png] Overview of the Rapid Response data.


[PMID 19956106OA-icon.png] Analysis of 19 genes for association with type I diabetes in the Type I Diabetes Genetics Consortium families.


[PMID 20072139OA-icon.png] Association of the AFF3 gene and IL2/IL21 gene region with juvenile idiopathic arthritis.


[PMID 20236493OA-icon.png] The contribution of genetic variation and infection to the pathogenesis of ANCA-associated systemic vasculitis.


[PMID 20300120] HLA and CTLA4 polymorphisms may confer a synergistic risk in the susceptibility to Graves' disease.


[PMID 20352109OA-icon.png] Association of the CTLA4 gene with Graves' disease in the Chinese Han population.


[PMID 20439292] Genetic variants in the prediction of rheumatoid arthritis.


[PMID 20444755OA-icon.png] Investigation of rheumatoid arthritis susceptibility genes identifies association of AFF3 and CD226 variants with response to anti-tumour necrosis factor treatment.


[PMID 20491567] CTLA4 CT60 single-nucleotide polymorphism is associated with Slovenian inflammatory bowel disease patients and regulates expression of CTLA4 isoforms.


[PMID 20557968] Association analysis of cytotoxic T-lymphocyte antigen 4 gene polymorphisms with primary biliary cirrhosis in Japanese patients.


[PMID 20610662OA-icon.png] Association of single nucleotide polymorphisms in cytotoxic T-lymphocyte antigen 4 and susceptibility to autoimmune type 1 diabetes in Tunisians.


[PMID 21383967OA-icon.png] Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci.


[PMID 21669243] CTLA-4, CD28, and ICOS gene polymorphism associations with non-small-cell lung cancer.


[PMID 22414241] Cytotoxic T-lymphocyte associated antigen-4 gene polymorphisms and primary biliary cirrhosis: A systematic review.


[PMID 22418270] Polymorphisms in cytotoxic T lymphocyte associated antigen-4 influence the rate of acute rejection after renal transplantation in 167 Chinese recipients.


[PMID 22511809] Association of variants in HLA-DQA1-DQB1, PTPN22, INS, and CTLA4 with GAD autoantibodies and insulin secretion in nondiabetic adults of the Botnia Prospective Study.


GET Evidence
rs3087243
aa_change
aa_change_short
impact pathogenic
qualified_impact Insufficiently evaluated pathogenic
overall_frequency 0.398438
summary



[PMID 23432218] Association between cytotoxic T-lymphocyte antigen 4 gene polymorphisms and primary biliary cirrhosis in Chinese population: data from a multicenter study


[PMID 23480667] Cytotoxic T-Lymphocyte Antigen-4 Genetic Variants and Risk of Ewing's Sarcoma


[PMID 23567921] Cytotoxic T-lymphocyte antigen 4 (CTLA4) +49AG and CT60 gene polymorphisms in Alopecia Areata: a case-control association study in the Italian population


[PMID 23597029OA-icon.png] The associations between the polymorphisms in the CTLA-4 gene and the risk of Graves' disease in the Chinese population


[PMID 23703660] The -319C/+49G/CT60G Haplotype of CTLA-4 Gene Confers Susceptibility to Rheumatoid Arthritis in Mexican Population


[PMID 24015180OA-icon.png] CTLA4 Gene Polymorphisms Influence the Incidence of Infection after Renal Transplantation in Chinese Recipients


[PMID 24270470] Influence of cytotoxic T lymphocyte-associated antigen 4 polymorphisms on the outcomes of hepatitis B virus infection


[PMID 24313821] Association of CTLA-4 Gene Polymorphism with End-Stage Renal Disease and Renal Allograft Outcome


[PMID 22328738OA-icon.png] Comprehensive assessment of rheumatoid arthritis susceptibility loci in a large psoriatic arthritis cohort.


[PMID 22891215OA-icon.png] Evidence of gene-gene interaction and age-at-diagnosis effects in type 1 diabetes.

GWAS snp
PMID [PMID 24390342OA-icon.png]
Trait Rheumatoid arthritis
Title Genetics of rheumatoid arthritis contributes to biology and drug discovery.
Risk Allele G
P-val 3E-25
Odds Ratio 1.14 [1.11-1.17]


[PMID 25940108OA-icon.png] A CT60G>A polymorphism in the CTLA-4 gene of the recipient may confer susceptibility to acute graft versus host disease after allogeneic hematopoietic stem cell transplantation


[PMID 26079279] HCV F protein amplifies the predictions of IL-28B and CTLA-4 polymorphisms about the susceptibility and outcomes of HCV infection in Southeast China


[PMID 26405547OA-icon.png] Association of the CTLA4 gene CT60/rs3087243 single-nucleotide polymorphisms with Graves' disease


[PMID 26403483] CTLA-4 and CD28 genes' polymorphisms and renal cell carcinoma susceptibility in the Polish population - a prospective study


[PMID 26656450] Variation in the CTLA4 3'UTR has phenotypic consequences for autoreactive T cells and associates with genetic risk for type 1 diabetes.


[PMID 27888068] Associations of single nucleotide polymorphisms of PTPN22 and Ctla4 genes with the risk of allergic rhinitis in a Chinese Han population.