|Title||Genome-wide assocation defines more than 30 distinct susceptibility loci for Crohn's disease|
|Odds Ratio||1.31 [NR]|
|Trait||Type 1 diabetes|
|Title||A genome-wide association study identifies KIAA0350 as a type 1 diabetes gene|
|Odds Ratio||1.80 [1.44-2.24]|
|Trait||Type 1 diabetes|
|Title||Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes|
|Odds Ratio||NR NR|
|Title||REL, encoding a member of the NF-kappaB family of transcription factors, is a newly defined risk locus for rheumatoid arthritis|
|Odds Ratio||NR NR|
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.
rs2476601 was confirmed in another 2007 study to be a risk factor for RA [PMID 17804836].
- [PMID 16490755] confirms the association of rs2476601 rheumatoid arthritis
- [PMID 15674368] two copies of the PTPN22 R620W allele more than doubles the risk for RF positive RA
- [PMID 15719322] see rs2476601(A;G)
- [PMID 15934099]
- [PMID 16052172]
- [PMID 16175503]
- [PMID 16185327]
- [PMID 16470599]
[PMID 17133608] associations of rs2476601 in PTPN22 R620W single-nucleotide polymorphism (SNP) with systemic sclerosis (SSc) or with anticentromere antibody (ACA)-positive or anti-topoisomerase I (anti-topo I) antibody-positive SSc, in a case-control study of US white, black, Hispanic, and Choctaw Indian individuals.
[PMID 17660222] studied ~300 UK patients with Behcet's disease and found that the R620W allele (i.e. rs2476601(A)) appeared to provide protection from Behcet's disease. The odds ratio for protection was calculated to be 2.4 (CI: 1.2 - 4.7).
[PMID 18200060] 1858T allele had an allelic odds ratio (OR) of 2.16 for generalized vitiligo and a genotypic OR of 2.35 as C/T heterozygotes. Similarly, individuals carrying the PTPN22 1858T allele had an allelic OR of 2.05 for the expanded autoimmunity phenotype, and a genotypic OR of 2.19 for C/T heterozygotes.
[PMID 18305142] rs2476601(A) has a higher relative risk in type-1 diabetes cases carrying lower risk HLA class II genotypes than in those carrying higher risk ones (p=1.36x10-4 in a test of interaction).
[PMID 18578611]] rs2476601 is not associated with Graves' disease in a study of Japanese patients.
[PMID 19357851] No association of PTPN22 gene polymorphism with rheumatoid arthritis in Turkey.
[PMID 21688149] Meta-analysis across 12 studies, totaling 4,300+ patients, concludes that there is an association between the rs2476601(A) allele and risk for systemic sclerosis, with an odds ratio of 1.169 (CI: 1.05 - 1.3, p = 0.004).Promethease reports for rs2476601 from Trait-o-matic are consistently finding this called as (A;G), while microarray results seem to follow the HapMap predictions. The source of this originates upstream in several different genotype callers:
This is probably triggered by the oddness of this dbSNP entry in which it is a C=>T in NM_012411.2 and a T=>C in NM_015967.3 and/or the fact NT_019273.18 was replaced by NT_032977
[PMID 19780033] Association of a functional polymorphism of PTPN22 encoding a lymphoid protein phosphatase in bilateral Meniere's disease
[PMID 19956106] Analysis of 19 genes for association with type I diabetes in the Type I Diabetes Genetics Consortium families
[PMID 19956096] rs2476601 T allele (R620W) defines high-risk PTPN22 type I diabetes-associated haplotypes with preliminary evidence for an additional protective haplotype
[PMID 20032229] Prediction of functional impairment and remission in rheumatoid arthritis patients by biochemical variables and genetic polymorphisms
[PMID 19951419] Confirmation of the genetic association of CTLA4 and PTPN22 with ANCA-associated vasculitis
|Title||Variant of TYR and Autoimmunity Susceptibility Loci in Generalized Vitiligo|
|Odds Ratio||1.39 [1.23-1.57]|
[PMID 20522204] PTPN22 gene regulates natural killer cell proliferation during in vitro expansion
|Title||Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk lock|
|Odds Ratio||1.94 [1.81-2.08]|
[PMID 20615141] Association of the Protein Tyrosine Phosphatase Nonreceptor 22 Haplotypes with Autoimmune Thyroid Disease in the Japanese Population
[PMID 20498205] Investigation of potential non-HLA rheumatoid arthritis susceptibility loci in a European cohort increases the evidence for nine markers
[PMID 21131644] Analysis of the influence of PTPN22 gene polymorphisms in systemic sclerosis
[PMID 21287672] Differential association of two PTPN22 coding variants with Crohn's disease and ulcerative colitis
[PMID 21384170] No association of PTPN22 R620 W gene polymorphism with rheumatic heart disease and systemic lupus erythematosus
[PMID 21410964] Association between the PTPN22 +1858 C/T polymorphism and psoriatic arthritis
[PMID 21724255] Functional polymorphisms in SOCS1 and PTPN22 genes correlate with the response to imatinib treatment in newly diagnosed chronic-phase chronic myeloid leukemia
[PMID 21965649] Evidence for PTPN2 R620W Polymorphism As the Sole Common Risk Variant for Rheumatoid Arthritis in the 1p13.2 Region
[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 22069277] Susceptibility influence of a PTPN22 haplotype with thyroid autoimmunity in Koreans
|Title||Genome-wide association analysis of autoantibody positivity in type 1 diabetes cases.|
|Odds Ratio||2.0000 [NR]|
[PMID 22427951] PTPN22.6, a Dominant Negative Isoform of PTPN22 and Potential Biomarker of Rheumatoid Arthritis
[PMID 22396730] No Association of PTPN22 Polymorphisms with Susceptibility to Ocular Behcet's Disease in Two Chinese Han Populations
[PMID 22632125] Evidence of cis-acting regulatory variation in PTPN22 in patients with rheumatoid arthritis
[PMID 22696186] The protein tyrosine phosphatase nonreceptor 22 C1858T polymorphism and vasculitis: a meta-analysis
[PMID 21922340] Combined influence of genetic and environmental factors in age of rheumatoid arthritis onset.
[PMID 22197427] PTPN22 and myasthenia gravis: replication in an Italian population and meta-analysis of literature data
[PMID 22743847] The +1858C/T PTPN22 gene polymorphism confers genetic susceptibility to rheumatoid arthritis in Mexican population from the Western Mexico
|Disease||Diabetes mellitus, Rheumatoid arthritis, Systemic lupus erythematosus, Hashimoto thyroiditis, Addison disease|
|CLNDBN||Diabetes mellitus, insulin-dependent, susceptibility to, Rheumatoid arthritis, Systemic lupus erythematosus, susceptibility to, Hashimoto thyroiditis, susceptibility to, Addison disease, susceptibility to|
|CLNSRC||OMIM Allelic Variant|
|CLNACC||RCV000009460.1, RCV000009461.1, RCV000009462.1, RCV000009463.1, RCV000009464.1|
[PMID 16380915] Replication of putative candidate-gene associations with rheumatoid arthritis in >4,000 samples from North America and Sweden: association of susceptibility with PTPN22, CTLA4, and PADI4.
[PMID 16464986] Lack of association between the protein tyrosine phosphatase non-receptor 22 (PTPN22)*620W allele and systemic sclerosis in the French Caucasian population.
[PMID 16945141] Fine mapping of genes within the IDDM8 region in rheumatoid arthritis.
[PMID 17000021] No independent role of the -1123 G>C and+2740 A>G variants in the association of PTPN22 with type 1 diabetes and juvenile idiopathic arthritis in two Caucasian populations.
[PMID 17044734] European population substructure: clustering of northern and southern populations.
[PMID 17148556] Association of PTPN22 haplotypes with Graves' disease.
[PMID 17170052] Investigation of genetic variation across the protein tyrosine phosphatase gene in patients with rheumatoid arthritis in the UK.
[PMID 17334650] 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 17579671] Association of PTPN22 single nucleotide polymorphism with rheumatoid arthritis but not with allergic asthma.
[PMID 17606874] Association of the vitamin D metabolism gene CYP27B1 with type 1 diabetes.
[PMID 17665434] Association of interleukin-6 and interleukin-10 genotypes with radiographic damage in rheumatoid arthritis is dependent on autoantibody status.
[PMID 17666451] 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 17683561] The TCF7L2 locus and type 1 diabetes.
[PMID 17868256] PTPN22 gene polymorphism in Behcet's disease.
[PMID 18075792] PTPN22: its role in SLE and autoimmunity.
[PMID 18248681] Prevalence of common disease-associated variants in Asian Indians.
[PMID 18292987] Joint effects of HLA, INS, PTPN22 and CTLA4 genes on the risk of type 1 diabetes.
[PMID 18310307] Genetic similarities between latent autoimmune diabetes in adults, type 1 diabetes, and type 2 diabetes.
[PMID 18341666] Polymorphisms in the PTPN22 region are associated with psoriasis of early onset.
[PMID 18375974] PTPN22 gene polymorphism in Takayasu's arteritis.
[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 18456185] Genetics and genomics of primary biliary cirrhosis.
[PMID 18462498] 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 18466461] Meta-genetic association of rheumatoid arthritis and PTPN22 using PedGenie 2.1.
[PMID 18466472] Constructing gene association networks for rheumatoid arthritis using the backward genotype-trait association (BGTA) algorithm.
[PMID 18466483] Modeling of PTPN22 and HLA-DRB1 susceptibility to rheumatoid arthritis.
[PMID 18466513] Evaluating gene x gene and gene x smoking interaction in rheumatoid arthritis using candidate genes in GAW15.
[PMID 18466529] Comparing strategies for evaluation of candidate genes in case-control studies using family data.
[PMID 18466531] Case-control association analysis of rheumatoid arthritis with candidate genes using related cases.
[PMID 18466535] Modeling the effect of PTPN22 in rheumatoid arthritis.
[PMID 18466554] Analyses of single marker and pairwise effects of candidate loci for rheumatoid arthritis using logistic regression and random forests.
[PMID 18466563] Classification of rheumatoid arthritis status with candidate gene and genome-wide single-nucleotide polymorphisms using random forests.
[PMID 18535005] The search for genes contributing to endometriosis risk.
[PMID 18556337] 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 18648537] A large-scale rheumatoid arthritis genetic study identifies association at chromosome 9q33.2.
[PMID 18668548] Genome-wide association study of rheumatoid arthritis in the Spanish population: KLF12 as a risk locus for rheumatoid arthritis susceptibility.
[PMID 18710467] The tryptophan 620 allele of the lymphoid tyrosine phosphatase (PTPN22) gene predisposes to autoimmune Addison's disease.
[PMID 18759295] The PTPN22 C1858T polymorphism is associated with skewing of cytokine profiles toward high interferon-alpha activity and low tumor necrosis factor alpha levels in patients with lupus.
[PMID 18776148] Joint genetic susceptibility to type 1 diabetes and autoimmune thyroiditis: from epidemiology to mechanisms.
[PMID 18794853] Common variants at CD40 and other loci confer risk of rheumatoid arthritis.
[PMID 18821667] The protein tyrosine phosphatase N22 gene is associated with juvenile and adult idiopathic inflammatory myopathy independent of the HLA 8.1 haplotype in British Caucasian patients.
[PMID 18978792] Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci.
[PMID 18987647] Rheumatoid arthritis: a view of the current genetic landscape.
[PMID 19068216] Investigation of Crohn's disease risk loci in ulcerative colitis further defines their molecular relationship.
[PMID 19073967] Shared and distinct genetic variants in type 1 diabetes and celiac disease.
[PMID 19098027] SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms.
[PMID 19119414] IL2RA genetic heterogeneity in multiple sclerosis and type 1 diabetes susceptibility and soluble interleukin-2 receptor production.
[PMID 19180256] Genotype analysis of polymorphisms in autoimmune susceptibility genes, CTLA-4 and PTPN22, in an acute anterior uveitis cohort.
[PMID 19180477] Genetic risk factors for rheumatoid arthritis differ in Caucasian and Korean populations.
[PMID 19188433] Do non-HLA genes influence development of persistent islet autoimmunity and type 1 diabetes in children with high-risk HLA-DR,DQ genotypes?
[PMID 19210888] Role of HLA-DRB1 and PTPN22 genes in susceptibility to juvenile idiopathic arthritis in Hungarian patients.
[PMID 19408013] Strategies and issues in the detection of pathway enrichment in genome-wide association studies.
[PMID 19445664] Association of common polymorphisms in known susceptibility genes with rheumatoid arthritis in a Slovak population using osteoarthritis patients as controls.
[PMID 19474294] Potential etiologic and functional implications of genome-wide association loci for human diseases and traits.
[PMID 19503742] Evaluation of PTPN22 polymorphisms and Vogt-Koyanagi-Harada disease in Japanese patients.
[PMID 19557189] Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions.
[PMID 19569043] Genome-wide association studies and the genetic dissection of complex traits.
[PMID 19591781] The search for lupus biomarkers.
[PMID 19682379] TagSNP transferability and relative loss of variability prediction from HapMap to an admixed population.
[PMID 19776214] SimCT: a generic tool to visualize ontology-based relationships for biological objects.
[PMID 19838195] A large-scale replication study identifies TNIP1, PRDM1, JAZF1, UHRF1BP1 and IL10 as risk loci for systemic lupus erythematosus.
[PMID 19923204] Genetic background of systemic sclerosis: autoimmune genes take centre stage.
[PMID 19924720] Analysis of multiple phenotypes.
[PMID 19956101] Overview of the Rapid Response data.
[PMID 19956109] The Type I Diabetes Genetics Consortium 'Rapid Response' family-based candidate gene study: strategy, genes selection, and main outcome.
[PMID 20017963] Representation of genetic association via attributable familial relative risks in order to identify polymorphisms functionally relevant to rheumatoid arthritis.
[PMID 20017967] Genome-wide association analyses of North American Rheumatoid Arthritis Consortium and Framingham Heart Study data utilizing genome-wide linkage results.
[PMID 20017974] Simultaneous analysis of all single-nucleotide polymorphisms in genome-wide association study of rheumatoid arthritis.
[PMID 20017985] Adjusting for HLA-DRbeta1 in a genome-wide association analysis of rheumatoid arthritis and related biomarkers.
[PMID 20017996] Effect of population stratification on the identification of significant single-nucleotide polymorphisms in genome-wide association studies.
[PMID 20018006] Case-control genome-wide association study of rheumatoid arthritis from Genetic Analysis Workshop 16 using penalized orthogonal-components regression-linear discriminant analysis.
[PMID 20018016] Application of seventeen two-locus models in genome-wide association studies by two-stage strategy.
[PMID 20018019] Two-stage joint selection method to identify candidate markers from genome-wide association studies.
[PMID 20018022] Replication of recently identified associated single-nucleotide polymorphisms from six autoimmune diseases in Genetic Analysis Workshop 16 rheumatoid arthritis data.
[PMID 20018025] Genome-wide analysis of haplotype interaction for the data from the North American Rheumatoid Arthritis Consortium.
[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 20018042] Assessment of genotype imputation methods.
[PMID 20018049] Evaluation of an optimal receiver operating characteristic procedure.
[PMID 20018053] A genome-wide association scan for rheumatoid arthritis data by Hotelling's T2 tests.
[PMID 20018054] Predictive modeling in case-control single-nucleotide polymorphism studies in the presence of population stratification: a case study using Genetic Analysis Workshop 16 Problem 1 dataset.
[PMID 20018057] Detecting single-nucleotide polymorphism by single-nucleotide polymorphism interactions in rheumatoid arthritis using a two-step approach with machine learning and a Bayesian threshold least absolute shrinkage and selection operator (LASSO) model.
[PMID 20018062] Identification of genes and haplotypes that predict rheumatoid arthritis using random forests.
[PMID 20018071] Allelic based gene-gene interactions in rheumatoid arthritis.
[PMID 20018074] Identifying rheumatoid arthritis susceptibility genes using high-dimensional methods.
[PMID 20018080] Effects of covariates and interactions on a genome-wide association analysis of rheumatoid arthritis.
[PMID 20018090] Comparative analysis of different approaches for dealing with candidate regions in the context of a genome-wide association study.
[PMID 20089178] Allelic variants in the PHTF1-PTPN22, C12orf30 and CD226 regions as candidate susceptibility factors for the type 1 diabetes in the Estonian population.
[PMID 20166877] Allele and haplotype frequency distribution in PTPN22 gene across variable ethnic groups: Implications for genetic association studies for autoimmune diseases.
[PMID 20236493] The contribution of genetic variation and infection to the pathogenesis of ANCA-associated systemic vasculitis.
[PMID 20353580] Evaluation of the rheumatoid arthritis susceptibility loci HLA-DRB1, PTPN22, OLIG3/TNFAIP3, STAT4 and TRAF1/C5 in an inception cohort.
[PMID 20403149] PTPN2 but not PTPN22 is associated with Crohn's disease in a New Zealand population.
[PMID 20439292] Genetic variants in the prediction of rheumatoid arthritis.
[PMID 20444268] Peripheral blood gene expression patterns discriminate among chronic inflammatory diseases and healthy controls and identify novel targets.
[PMID 20696024] PTPN22 polymorphism is related to autoimmune disease risk in patients with Turner syndrome.
[PMID 20722033] The susceptibility loci juvenile idiopathic arthritis shares with other autoimmune diseases extend to PTPN2, COG6, and ANGPT1.
[PMID 21078766] The association between the PTPN22 C1858T polymorphism and systemic lupus erythematosus: a meta-analysis update.
[PMID 21193990] A PTPN22 promoter polymorphism -1123G>C is associated with RA pathogenesis in Chinese.
[PMID 21304977] An investigation of genome-wide studies reported susceptibility loci for ulcerative colitis shows limited replication in north Indians.
[PMID 21379322] Risk alleles for systemic lupus erythematosus in a large case-control collection and associations with clinical subphenotypes.
[PMID 21383967] Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci.
[PMID 21408207] Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production.
[PMID 21506938] Association of the PTPN22 gene polymorphism with autoantibody positivity in Turkish rheumatoid arthritis patients.
[PMID 21570397] Susceptibility to amoxicillin-clavulanate-induced liver injury is influenced by multiple HLA class I and II alleles.
[PMID 21752868] PTPN22 R620W genotype-phenotype correlation analysis and gene-environment interaction study in early rheumatoid arthritis: results from the ESPOIR cohort.
[PMID 22210423] Lack of association of the rs2476601 PTPN22 gene polymorphism with transplanted kidney function.
[PMID 22327470] The association between the functional PTPN22 1858 C/T and MIF -173 C/G polymorphisms and juvenile idiopathic arthritis: a meta-analysis.
[PMID 22493691] Novel associations for hypothyroidism include known autoimmune risk loci.
[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.
[PMID 22544573] PTPN22 C1858T and the risk of psoriasis: a meta-analysis.
|qualified_impact||Insufficiently evaluated not reviewed|
|Title||Risk for myasthenia gravis maps to a (151) Pro→Ala change in TNIP1 and to human leukocyte antigen-B*08.|
|Odds Ratio||1.71 [1.44-2.02]|
|Title||Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.|
|Odds Ratio||1.26 [1.17-1.37]|
[PMID 23946333] Identification of the PTPN22 functional variant R620W as susceptibility genetic factor for giant cell arteritis
[PMID 23944755] The impact of CTLA4 and PTPN22 genes polymorphisms on long-term renal allograft function and transplant outcomes
[PMID 23950893] PTPN22 Association in Systemic Lupus Erythematosus (SLE) with Respect to Individual Ancestry and Clinical Sub-Phenotypes
[PMID 23974994] Replication Study of Ulcerative Colitis Risk Loci in a Lithuanian-Latvian Case-Control Sample
[PMID 24160187] Meta-analysis confirms association between TNFA-G238A variant and JIA, and between PTPN22-C1858T variant and oligoarticular, RF-polyarticular and RF-positive polyarticular JIA
[PMID 23582631] Pathway analysis of genome-wide association studies on rheumatoid arthritis
[PMID 24386393] Genetic Heterogeneity of Susceptibility Gene in Different Ethnic Populations: Refining Association Study of PTPN22 for Graves' Disease in a Chinese Han Population
[PMID 24103478] Contribution of PTPN22, CD28, CTLA-4 and ZAP-70 variants to the risk of type 1 diabetes in Tunisians