rs7574865
| Orientation | plus |
| Stabilized | plus |
| Geno | Mag | Summary |
|---|---|---|
| (G;G) | 1 | normal risk of rheumatoid arthritis, SLE, Sjögren's syndrome, type-1 diabetes, and primary biliary cirrhosis. |
| (G;T) | 2.5 | 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. |
| (T;T) | 3.5 | 1.69x risk of rheumatoid arthritis; 2.4x risk of SLE; 2.28x risk of Sjögren's syndrome; increased risk of type-1 diabetes; and increased risk of primary biliary cirrhosis. |
| Reference | GRCh38 38.1/141 |
| Chromosome | 2 |
| Position | 191099907 |
| Gene | STAT4 |
| is a | snp |
| is | mentioned by |
| dbSNP | rs7574865 |
| dbSNP (classic) | rs7574865 |
| ClinGen | rs7574865 |
| ebi | rs7574865 |
| HLI | rs7574865 |
| Exac | rs7574865 |
| Gnomad | rs7574865 |
| Varsome | rs7574865 |
| LitVar | rs7574865 |
| Map | rs7574865 |
| PheGenI | rs7574865 |
| Biobank | rs7574865 |
| 1000 genomes | rs7574865 |
| hgdp | rs7574865 |
| ensembl | rs7574865 |
| geneview | rs7574865 |
| scholar | rs7574865 |
| rs7574865 | |
| pharmgkb | rs7574865 |
| gwascentral | rs7574865 |
| openSNP | rs7574865 |
| 23andMe | rs7574865 |
| SNPshot | rs7574865 |
| SNPdbe | rs7574865 |
| MSV3d | rs7574865 |
| GWAS Ctlg | rs7574865 |
| GMAF | 0.2493 |
| Max Magnitude | 3.5 |
| ? | (G;G) (G;T) (T;T) | 28 |
|---|---|---|
|
| ||
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.[PMID 20169389]
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." [PMID 17804842
]
A study of 124 Caucasian patients with primary Sjögren's syndrome, an autoimmune disease related to RA and SLE, also found the rs7574865(T) allele to be associated with higher risk for this condition (p=0.01). The GT genotype is associated with 1.42x and the TT with 2.28x odds. [PMID 18273036]
[PMID 18516230] associated with SLE characterized by double-stranded DNA autoantibodies (MAF = 35.1%, OR = 1.86, p<10(-19)), nephritis (MAF = 34.3%, OR = 1.80, p<10(-11)), and age at diagnosis<30 years (MAF = 33.8%, OR = 1.77, p<10(-13))
[PMID 18576330] The combined ORs for RA and SLE, respectively, were 1.27 (P = 8.4 x 10(-9)) and 1.61 (P = 2.1 x 10(-11)) for allele frequency distribution; these ORs in the Japanese were quite similar to those previously observed in the Caucasian population
[PMID 18576336] RA risk associated with rs7574865(T) allele was also found in studies of 923 Spanish, 273 Swedish, and 876 Dutch patients.
[PMID 18703106] The rs7574865(T) allele is associated with increased risk for type-1 diabetes; the odds ratio is 1.94, CI: 1.29-2.91, p = 0.0012, based on a study of Greek patients.
A study of RA patients from Crete also found that the rs7574865(T) allele represented increased risk for rheumatoid arthritis.[PMID 18625278]
[PMID 18759272] A study of 2,776 Spanish subjects found that the rs7574865(T) allele was associated with rheumatoid arthritis, Crohn's disease, ulcerative colitis, and type-1 diabetes, but not with multiple sclerosis.
[PMID 19332627] Lack of Association Between STAT4 Gene Polymorphism and Biopsy-proven Giant Cell Arteritis
| GWAS snp | |
|---|---|
| PMID | [PMID 18204098] |
| Trait | Systemic lupus erythematosus |
| Title | Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX |
| Risk Allele | T |
| P-val | 8.9999999999999995E-14 |
| Odds Ratio | NR NR |
[PMID 19479340] Association of STAT4 polymorphism with rheumatoid arthritis and systemic lupus erythematosus: a meta-analysis
[PMID 19500629] STAT4 gene polymorphism is associated with psoriasis in the genetically homogeneous population of Crete, Greece
[PMID 19565500] Variants in TNFAIP3, STAT4, and C12orf30 loci associated with multiple autoimmune diseases are also associated with juvenile idiopathic arthritis
[PMID 19404967] Confirmation of STAT4, IL2/IL21, and CTLA4 polymorphisms in rheumatoid arthritis
[PMID 19588142] Association between the rs7574865 polymorphism of STAT4 and rheumatoid arthritis: a meta-analysis
[PMID 19644887] STAT4 is a genetic risk factor for systemic sclerosis having additive effects with IRF5 on disease susceptibility and related pulmonary fibrosis
[PMID 19714582] Rheumatoid arthritis does not share most of the newly identified systemic lupus erythematosus genetic factors
[PMID 19737838] A haplotype in STAT4 gene associated with rheumatoid arthritis in Caucasians is not associated in the Han Chinese population, but with the presence of rheumatoid factor
[PMID 19644876] Association of STAT4 and BLK, but not BANK1 or IRF5, with primary antiphospholipid syndrome
| GWAS snp | |
|---|---|
| PMID | [PMID 19838193] |
| Trait | Systemic lupus erythematosus |
| Title | Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus |
| Risk Allele | A |
| P-val | 5E-42 |
| Odds Ratio | 1.51 [1.43-1.61] |
[PMID 20039785] The Protein Tyrosine Phosphatase, Non-Receptor Type 22 R620W Polymorphism Does Not Confer Susceptibility to Psoriasis in the Genetic Homogeneous Population of Crete
[PMID 19877059] BANK1 is a genetic risk factor for diffuse cutaneous systemic sclerosis and has additive effects with IRF5 and STAT4
[PMID 19684152] Cigarette smoking, STAT4 and TNFRSF1B polymorphisms, and systemic lupus erythematosus in a Japanese population
[PMID 20176035] Association of signal transducer and activator of transcription 4 genetic variants with extra-intestinal manifestations in inflammatory bowel disease
[PMID 20438790] STAT4 polymorphism in a Chinese Han Population with Vogt-Koyanagi-Harada syndrome and Behcet's disease
| GWAS snp | |
|---|---|
| PMID | [PMID 20453841] |
| Trait | Rheumatoid arthritis |
| Title | A regulatory variant in CCR6 is associated with rheumatoid arthritis susceptibility |
| Risk Allele | T |
| P-val | 0.000002 |
| Odds Ratio | 1.17 [1.10-1.25] |
| GWAS snp | |
|---|---|
| PMID | [PMID 20453842]
|
| Trait | Rheumatoid arthritis |
| Title | Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk lock |
| Risk Allele | T |
| P-val | 3E-7 |
| Odds Ratio | 1.16 [1.10-1.23] |
[PMID 20498205] Investigation of potential non-HLA rheumatoid arthritis susceptibility loci in a European cohort increases the evidence for nine markers
[PMID 21163111] Variation in STAT4 is associated with systemic lupus erythematosus in Chinese Northern Han population
[PMID 21237270] Polymorphisms in STAT4 Increase the Risk of acute renal allograft rejection in the Chinese population
[PMID 21418779] Signal transducer and activator of transcription and the risk of rheumatoid arthritis and thyroid autoimmune disorders
| GWAS snp | |
|---|---|
| PMID | [PMID 21383967]
|
| Trait | |
| Title | Meta-Analysis of Genome-Wide Association Studies in Celiac Disease and Rheumatoid Arthritis Identifies Fourteen Non-HLA Shared Loci |
| Risk Allele | T |
| P-val | 4E-10 |
| Odds Ratio | None None |
| GWAS snp | |
|---|---|
| PMID | [PMID 21408207]
|
| Trait | |
| Title | Differential Genetic Associations for Systemic Lupus Erythematosus Based on Anti-dsDNA Autoantibody Production |
| Risk Allele | T |
| P-val | 0.000008 |
| Odds Ratio | 1.4100 [1.21-1.63] |
[PMID 21683716] Signal transducer and activator of transcription 4 gene polymorphisms associated with rheumatoid arthritis in Northwestern Chinese Han population
| GWAS snp | |
|---|---|
| PMID | [PMID 21750679]
|
| Trait | |
| Title | Genome-wide scan identifies TNIP1, PSORS1C1, and RHOB as novel risk loci for systemic sclerosis. |
| Risk Allele | T |
| P-val | 2E-13 |
| Odds Ratio | 1.3800 [1.27-1.50] |
[PMID 21968398] TRAF1/C5, eNOS, C1q, but not STAT4 and PTPN22 gene polymorphisms are associated with genetic susceptibility to systemic lupus erythematosus in Turkey
[PMID 22133489] The polymorphisms of T cell-specific TBX21 and STAT4 genes may contribute to the susceptibility of Chinese individuals to aplastic anemia
[PMID 22173230] A meta-analysis of the association between cytokine gene polymorphisms and systemic sclerosis
[PMID 22483685] Interactions between IL17A, IL23R, and STAT4 polymorphisms confer susceptibility to intestinal Behcet's disease in Korean population
[PMID 22714917] Association of STAT4 rs7574865 polymorphism with autoimmune diseases: a meta-analysis
[PMID 17932559] Association of STAT4 with rheumatoid arthritis in the Korean population.
[PMID 18432273] STAT4 but not TRAF1/C5 variants influence the risk of developing rheumatoid arthritis and systemic lupus erythematosus in Colombians.
[PMID 18434327] Re-evaluation of putative rheumatoid arthritis susceptibility genes in the post-genome wide association study era and hypothesis of a key pathway underlying susceptibility.
[PMID 18579578] A risk haplotype of STAT4 for systemic lupus erythematosus is over-expressed, correlates with anti-dsDNA and shows additive effects with two risk alleles of IRF5.
[PMID 18794853] Common variants at CD40 and other loci confer risk of rheumatoid arthritis.
[PMID 18803832] Role of STAT4 polymorphisms in systemic lupus erythematosus in a Japanese population: a case-control association study of the STAT1-STAT4 region.
[PMID 19019891] STAT4 associates with systemic lupus erythematosus through two independent effects that correlate with gene expression and act additively with IRF5 to increase risk.
[PMID 19109131] Cutting edge: autoimmune disease risk variant of STAT4 confers increased sensitivity to IFN-alpha in lupus patients in vivo.
[PMID 19116934] The chromosome 7q region association with rheumatoid arthritis in females in a British population is not replicated in a North American case-control series.
[PMID 19120275] STAT4 polymorphism is associated with early-onset type 1 diabetes, but not with late-onset type 1 diabetes.
[PMID 19225526] Population differences in SLE susceptibility genes: STAT4 and BLK, but not PXK, are associated with systemic lupus erythematosus in Hong Kong Chinese.
[PMID 19286670] The STAT4 gene influences the genetic predisposition to systemic sclerosis phenotype.
[PMID 19287509] Genome-wide association study of determinants of anti-cyclic citrullinated peptide antibody titer in adults with rheumatoid arthritis.
[PMID 19333953] High-density genotyping of STAT4 reveals multiple haplotypic associations with systemic lupus erythematosus in different racial groups.
[PMID 19371230] STAT4 is not associated with type 2 diabetes in the genetically homogeneous population of Crete.
[PMID 19442287] Replication of recently identified systemic lupus erythematosus genetic associations: a case-control study.
[PMID 19445664] Association of common polymorphisms in known susceptibility genes with rheumatoid arthritis in a Slovak population using osteoarthritis patients as controls.
[PMID 19458352] Primary biliary cirrhosis associated with HLA, IL12A, and IL12RB2 variants.
[PMID 19591781] The search for lupus biomarkers.
[PMID 19605742] STAT4 single nucleotide polymorphism, rs7574865 G/T, as a risk for antiphospholipid syndrome.
[PMID 19674979] Overlap of disease susceptibility loci for rheumatoid arthritis and juvenile idiopathic arthritis.
[PMID 19838195] A large-scale replication study identifies TNIP1, PRDM1, JAZF1, UHRF1BP1 and IL10 as risk loci for systemic lupus erythematosus.
[PMID 19849816] Genetics of rheumatic disease.
[PMID 19923204] Genetic background of systemic sclerosis: autoimmune genes take centre stage.
[PMID 20018027] Conditional analysis of the major histocompatibility complex in rheumatoid arthritis.
[PMID 20018035] A combinatorial approach for detecting gene-gene interaction using multiple traits of Genetic Analysis Workshop 16 rheumatoid arthritis data.
[PMID 20018049] Evaluation of an optimal receiver operating characteristic procedure.
[PMID 20153791] STAT4 gene influences genetic predisposition to ulcerative colitis but not Crohn's disease in the Spanish population: a replication study.
[PMID 20169177] Genome-wide association study in Asian populations identifies variants in ETS1 and WDFY4 associated with systemic lupus erythematosus.
[PMID 20353580] Evaluation of the rheumatoid arthritis susceptibility loci HLA-DRB1, PTPN22, OLIG3/TNFAIP3, STAT4 and TRAF1/C5 in an inception cohort.
[PMID 20360187] Influence of STAT4 polymorphism in primary Sjogren's syndrome.
[PMID 20439292] Genetic variants in the prediction of rheumatoid arthritis.
[PMID 20444755] Investigation of rheumatoid arthritis susceptibility genes identifies association of AFF3 and CD226 variants with response to anti-tumour necrosis factor treatment.
[PMID 20454450] Evidence for STAT4 as a common autoimmune gene: rs7574865 is associated with colonic Crohn's disease and early disease onset.
[PMID 20652065] Interferon alpha in systemic lupus erythematosus.
[PMID 20722033] The susceptibility loci juvenile idiopathic arthritis shares with other autoimmune diseases extend to PTPN2, COG6, and ANGPT1.
[PMID 21149496] NLRP1 influences the systemic sclerosis phenotype: a new clue for the contribution of innate immunity in systemic sclerosis-related fibrosing alveolitis pathogenesis.
[PMID 21167895] Association of genetic variations in the STAT4 and IRF7/KIAA1542 regions with systemic lupus erythematosus in a Northern Han Chinese population.
[PMID 21379322] Risk alleles for systemic lupus erythematosus in a large case-control collection and associations with clinical subphenotypes.
[PMID 21922340] Combined influence of genetic and environmental factors in age of rheumatoid arthritis onset.
[PMID 22569826] Abnormal Genetic and Epigenetic Changes in Signal Transducer and Activator of Transcription 4 in the Pathogenesis of Inflammatory Bowel Diseases.
| GWAS snp | |
|---|---|
| PMID | [PMID 23053960] |
| Trait | Systemic lupus erythematosus |
| Title | Genome-wide pathway analysis of genome-wide association studies on systemic lupus erythematosus and rheumatoid arthritis. |
| Risk Allele | T |
| P-val | 4E-14 |
| Odds Ratio | 1.48 [1.335-1.634] |
| GWAS snp | |
|---|---|
| PMID | [PMID 23000144]
|
| Trait | Primary biliary cirrhosis |
| Title | Genome-wide association study identifies TNFSF15 and POU2AF1 as susceptibility loci for primary biliary cirrhosis in the Japanese population. |
| Risk Allele | T |
| P-val | 1E-6 |
| Odds Ratio | 1.35 [1.19-1.52] |
| GWAS snp | |
|---|---|
| PMID | [PMID 23273568]
|
| Trait | Systemic lupus erythematosus |
| Title | Meta-analysis followed by replication identifies loci in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as associated with systemic lupus erythematosus in Asians. |
| Risk Allele | T |
| P-val | 1E-21 |
| Odds Ratio | 1.63 |
| GWAS snp | |
|---|---|
| PMID | [PMID 23242368]
|
| Trait | Hepatocellular carcinoma (hepatitis B virus related) |
| Title | Genetic variants in STAT4 and HLA-DQ genes confer risk of hepatitis B virus-related hepatocellular carcinoma. |
| Risk Allele | G |
| P-val | 2E-10 |
| Odds Ratio | 1.21 [1.14-1.28] |
[PMID 23727609] Replication study of STAT4 rs7574865 G/T polymorphism and risk of rheumatoid arthritis in a Chinese population
[PMID 23755762] STAT4 is a genetic risk factor for systemic sclerosis in a Chinese population
[PMID 23912645] Association of STAT4 rs7574865 with Susceptibility to Systemic Lupus Erythematosus in Iranian Population
[PMID 24023622] Analysis of Gender Differences in Genetic Risk: Association of TNFAIP3 Polymorphism with Male Childhood-Onset Systemic Lupus Erythematosus in the Japanese Population
[PMID 23360093] Association study of STAT4 polymorphisms and type 1 diabetes in Northeastern Chinese Han population
[PMID 24059108] [Signal transducer and activator of transcription 4 gene polymorphisms associated with dilated cardiomyopathy in Chinese Han population]
[PMID 22328738] Comprehensive assessment of rheumatoid arthritis susceptibility loci in a large psoriatic arthritis cohort.
[PMID 22402141] Positive association between STAT4 polymorphisms and polymyositis/dermatomyositis in a Japanese population.
[PMID 22753649] Variants within STAT genes reveal association with anticitrullinated protein antibody-negative rheumatoid arthritis in 2 European populations.
[PMID 22968431] Limited contribution of common genetic variants to risk for liver injury due to a variety of drugs.
[PMID 23295549] Association between polymorphism in STAT4 gene and risk of rheumatoid arthritis: a meta-analysis.
[PMID 23450725] Susceptibility to childhood-onset rheumatoid arthritis: investigation of a weighted genetic risk score that integrates cumulative effects of variants at five genetic loci.
[PMID 23628400] Meta-analysis reveals an association of STAT4 polymorphisms with systemic autoimmune disorders and anti-dsDNA antibody.
[PMID 23777930] Investigation of juvenile idiopathic arthritis susceptibility loci: results from a Greek population.
[PMID 24204805] Replication of genome wide association studies on hepatocellular carcinoma susceptibility loci in a Chinese population
[PMID 25097569] Association of STAT4 gene rs7574865G > T polymorphism with ulcerative colitis risk: evidence from 1532 cases and 3786 controls
| GWAS snp | |
|---|---|
| PMID | [PMID 24871463]
|
| Trait | Systemic lupus erythematosus |
| Title | GWAS identifies novel SLE susceptibility genes and explains the association of the HLA region. |
| Risk Allele | T |
| P-val | 5E-9 |
| Odds Ratio | 1.51 [1.41-1.62] |
[PMID 24741605] Insight into gene polymorphisms involved in toll-like receptor/interferon signalling pathways for systemic lupus erythematosus in South East Asia
| ClinVar | |
|---|---|
| Risk | Rs7574865(G;G) |
| Alt | Rs7574865(G;G) |
| Reference | Rs7574865(T;T) |
| Significance | Other |
| Disease | Systemic lupus erythematosus 11 |
| Variation | info |
| Gene | STAT4 |
| CLNDBN | Systemic lupus erythematosus 11 |
| Reversed | 0 |
| HGVS | NC_000002.11:g.191964633T\x3d |
| CLNSRC | OMIM Allelic Variant |
| CLNACC | RCV000024612.3, |
[PMID 25664124] Genetic variants of STAT4 are associated with ankylosing spondylitis susceptibility and severity in a Chinese Han population
[PMID 25781893] STAT4 rs7574865 G/T and PTPN22 rs2488457 G/C Polymorphisms Influence the Risk of Developing Juvenile Idiopathic Arthritis in Han Chinese Patients
[PMID 25913043] Replication of genome wide association studies on hepatocellular carcinoma susceptibility loci of STAT4 and HLA-DQ in a Korean population
[PMID 26399911] Associations between interleukin and interleukin receptor gene polymorphisms and risk of gout
[PMID 26538132] Genetic variations in STAT4,C2,HLA-DRB1 and HLA-DQ associated with risk of hepatitis B virus-related liver cirrhosis
[PMID 26745093] Single Nucleotide Polymorphisms in STAT3 and STAT4 and Risk of Hepatocellular Carcinoma in Thai Patients with Chronic Hepatitis B.
[PMID 27126090] Meta-analysis reveals an association of STAT4 polymorphism with hepatocellular carcinoma risk.
[PMID 27234231] STAT4 rs7574865 G/T polymorphism is associated with rheumatoid arthritis and disease activity, but not with anti-CCP antibody levels in a Mexican population.
[PMID 27342690] Polymorphisms in STAT4, IL10, PSORS1C1, PTPN2 and MIR146A genes are differently associated with prognostic factors in Italian patients affected by Rheumatoid Arthritis.
[PMID 27394003] Association of HLA-DP/DQ and STAT4 polymorphisms with ankylosing spondylitis in Southwest China.
[PMID 28524764] Lack of Association between STAT4 Single Nucleotide Polymorphisms and Iranian Juvenile Rheumatoid Arthritis Patients.
[PMID 28670251] Genetic similarities and differences between discoid and systemic lupus erythematosus patients within the Polish population.
[PMID 28852993] STAT4 Polymorphisms are Associated with Neuromyelitis Optica Spectrum Disorders.
[PMID 29276866] Association of STAT4 gene single nucleotide polymorphisms with Iranian juvenile-onset systemic lupus erythematosus patients.
[PMID 29467950] Genetic polymorphisms in HLA-DP and STAT4 are associated with IgA nephropathy in a Southwest Chinese population.
[PMID 30289982] PNPLA3 and TM6SF2 variants as risk factors of hepatocellular carcinoma across various etiologies and severity of underlying liver diseases.
[PMID 30463656] [STAT4 rs7574865 polymorphism is associated with the susceptibility of rheumatoid arthritis in Wuling mountain area].
[PMID 30864557] Studying the Association between STAT4 Gene Polymorphism and Susceptibility to Rheumatoid Arthritis Disease: An Updated Meta-Analysis.
[PMID 30882006] STAT4, TRAF3IP2, IL10, and HCP5 Polymorphisms in Sjögren's Syndrome: Association with Disease Susceptibility and Clinical Aspects.
[PMID 31149782] Polymorphisms in MAPK9 (rs4147385) and CSF1R (rs17725712) are associated with the development of inhibitors in patients with haemophilia A in North China.
[PMID 31916109] Defining genetic risk factors for scleroderma-associated interstitial lung disease : IRF5 and STAT4 gene variants are associated with scleroderma while STAT4 is protective against scleroderma-associated interstitial lung disease.
