{{Rsnum
|rsid=2476601
|Gene=PTPN22
|Chromosome=1
|position=113834946
|Orientation=plus
|ReferenceAllele=C
|MissenseAllele=T
|GMAF=0.04224
|Assembly=GRCh38
|GenomeBuild=38.1
|dbSNPBuild=141
|geno1=(A;A)
|geno2=(A;G)
|geno3=(G;G)
|Gene_s=PTPN22,RP5-1073O3.2
}}{{ population diversity
| geno1=(A;A)
| geno2=(A;G)
| geno3=(G;G)
| CEU | 0.9 | 21.6 | 77.5
| HCB | 0.0 | 3.0 | 97.0
| JPT | 0.0 | 6.3 | 93.7
| YRI | 0.0 | 1.4 | 98.6
| ASW | 0.0 | 3.6 | 96.4
| CHB | 0.0 | 3.0 | 97.0
| CHD | 0.0 | 2.8 | 97.2
| GIH | 0.0 | 2.0 | 98.0
| LWK | 0.0 | 2.7 | 97.3
| MEX | 1.8 | 7.0 | 91.2
| MKK | 0.6 | 0.6 | 98.7
| TSI | 0.0 | 13.3 | 86.7
| HapMapRevision=28
}}{{PMID Auto GWAS
|PMID=18587394
|Trait=Crohn's disease
|Title=Genome-wide assocation defines more than 30 distinct susceptibility loci for Crohn's disease
|RiskAllele=G
|Pval=1E-8
|OR=1.31
|ORtxt=[NR]
|OA=1
}}{{PMID Auto GWAS
|PMID=17632545
|Trait=Type 1 diabetes
|Title=A genome-wide association study identifies KIAA0350 as a type 1 diabetes gene
|RiskAllele=A
|Pval=9.9999999999999995E-8
|OR=1.80
|ORtxt=[1.44-2.24]
}}{{PMID Auto GWAS
|PMID=19430480
|Trait=Type 1 diabetes
|Title=Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes
|RiskAllele=
|Pval=9E-85
|OR=NR
|ORtxt=NR
|OA=1
}}{{PMID Auto GWAS
|PMID=19503088
|Trait=Rheumatoid arthritis
|Title=REL, encoding a member of the NF-kappaB family of transcription factors, is a newly defined risk locus for rheumatoid arthritis
|RiskAllele=
|Pval=2E-21
|OR=NR
|ORtxt=NR
|OA=1
}}

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). {{PMID|17554260|OA=1
}}

[[rs2476601]] was confirmed in another 2007 study to be a risk factor for RA {{PMID|17804836|OA=1
}}.

*{{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|OA=1
}} see [[rs2476601(A;G)]]
*{{PMID|15934099}} 
*{{PMID|16052172}} 
*{{PMID|16175503|OA=1
}} 
*{{PMID|16185327}} 
*{{PMID|16470599}}

[[rs2476601]] shows a 0.75 (r squared) correlation with [[rs6679677]], a SNP in the [[RSBN1]] gene associated with [[rheumatoid arthritis]]. {{PMID|17554300|OA=1
}}

{{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|OA=1
}} 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|17934143}}] Confirms association of [[rs2476601]] with [[type-1 diabetes]] in a Sardinian population of 490 sporadic patients (794 families).

{{PMID|18301444}} In study of 332 Norwegian patients plus a meta-analysis, the [[rs2476601]](A) allele was linked to autoimmune [[Addison's disease]] (p=0.003)

{{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<sup>-4</sup> in a test of interaction).

{{PMID|18578611}}] [[rs2476601]] is not associated with Graves' disease in a study of Japanese patients.

{{PMID|18576360}} [[rs2476601]](A) allele is associated with (slightly) increased risk for [[systemic sclerosis]] in European Caucasians.

[http://blog.23andme.com/2008/12/12/snpwatch-type-1-diabetes-and-celiac-disease-share-some-genetic-risk-factors/ 23andMe blog] rs2476601(A) increases the risk of [[type 1 diabetes]] and [[rheumatoid arthritis]], but has shown to be protective for [[Crohn's disease]].

{{PMID|19210878}} Women with (T;T) and (C;T) genotypes displayed a 2x increased risk of [[systemic lupus erythematosus]] (95% CI=1.324 - 3.070, P=0.0014)

{{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).

{{omim
|desc=DIABETES MELLITUS, INSULIN-DEPENDENT, SUSCEPTIBILITY TO
|id=600716
|quiet=1
|rsnum=2476601
|variant=0001
}}
{{omim
|desc=HYPOADRENOCORTICISM, FAMILIAL
|id=240200
|rsnum=2476601
}}

[[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:
*maq
*SoapSNP
*AB_SOLiD_SNP_caller
*JW
*NA18507
*SIQ2
*CV
*GSNAP

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 Auto
|PMID=19780033
|Title=Association of a functional polymorphism of PTPN22 encoding a lymphoid protein phosphatase in bilateral Meniere's disease
}}

{{PMID Auto
|PMID=19956106
|Title=Analysis of 19 genes for association with type I diabetes in the Type I Diabetes Genetics Consortium families
|OA=1
}}
{{PMID Auto
|PMID=19956096
|Title=rs2476601 T allele (R620W) defines high-risk PTPN22 type I diabetes-associated haplotypes with preliminary evidence for an additional protective haplotype
|OA=1
}}

{{PharmGKB
|RSID=rs2476601
|Name_s=
|Gene_s=PTPN22
|Feature=
|Evidence=PubMed ID:17982455
|Annotation=This SNP has been strongly associated with risk of rheumatoid arthritis.
|Drugs=
|Drug Classes=
|Diseases=Arthritis, Rheumatoid
|Curation Level=Curated
|PharmGKB Accession ID=PA161613788
}}
{{PMID Auto
|PMID=20032229
|Title=Prediction of functional impairment and remission in rheumatoid arthritis patients by biochemical variables and genetic polymorphisms
}}

{{PMID Auto
|PMID=19951419
|Title=Confirmation of the genetic association of CTLA4 and PTPN22 with ANCA-associated vasculitis
|OA=1
}}

{{PMID Auto GWAS
|PMID=20410501
|Trait=Vitiligo
|Title=Variant of TYR and Autoimmunity Susceptibility Loci in Generalized Vitiligo
|RiskAllele=A
|Pval=1E-7
|OR=1.39
|ORtxt=[1.23-1.57]
|OA=1
}}
{{PMID Auto
|PMID=20522204
|Title=PTPN22 gene regulates natural killer cell proliferation during in vitro expansion
}}
{{PMID Auto GWAS
|PMID=20453842
|Trait=Rheumatoid arthritis
|Title=Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk lock
|RiskAllele=A
|Pval=9E-74
|OR=1.94
|ORtxt=[1.81-2.08]
}}
{{PMID Auto
|PMID=20615141
|Title=Association of the Protein Tyrosine Phosphatase Nonreceptor 22 Haplotypes with Autoimmune Thyroid Disease in the Japanese Population
}}
{{PMID Auto
|PMID=20498205
|Title=Investigation of potential non-HLA rheumatoid arthritis susceptibility loci in a European cohort increases the evidence for nine markers
|OA=1
}}
{{PMID Auto
|PMID=21131644
|Title=Analysis of the influence of PTPN22 gene polymorphisms in systemic sclerosis
|OA=1
}}

{{PMID Auto
|PMID=21287672
|Title=Differential association of two PTPN22 coding variants with Crohn's disease and ulcerative colitis
}}

{{omim
|id=152700
|rsnum=2476601
}}

{{omim
|id=222100
|rsnum=2476601
}}

{{PMID Auto
|PMID=21384170
|Title=No association of PTPN22 R620 W gene polymorphism with rheumatic heart disease and systemic lupus erythematosus
}}

{{PMID Auto
|PMID=21410964
|Title=Association between the PTPN22 +1858 C/T polymorphism and psoriatic arthritis
|OA=1
}}

{{PMID Auto
|PMID=21724255
|Title=Functional polymorphisms in SOCS1 and PTPN22 genes correlate with the response to imatinib treatment in newly diagnosed chronic-phase chronic myeloid leukemia
}}

{{PMID Auto
|PMID=21965649
|Title=Evidence for PTPN2 R620W Polymorphism As the Sole Common Risk Variant for Rheumatoid Arthritis in the 1p13.2 Region
}}

{{PMID Auto
|PMID=21968398
|Title=TRAF1/C5, eNOS, C1q, but not STAT4 and PTPN22 gene polymorphisms are associated with genetic susceptibility to systemic lupus erythematosus in Turkey
}}

{{PMID Auto
|PMID=22069277
|Title=Susceptibility influence of a PTPN22 haplotype with thyroid autoimmunity in Koreans
}}

{{PMID Auto GWAS
|PMID=21829393
|Trait=None
|Title=Genome-wide association analysis of autoantibody positivity in type 1 diabetes cases.
|RiskAllele=A
|Pval=2E-111
|OR=2.0000
|ORtxt=[NR]
|OA=1
}}

{{PMID Auto
|PMID=22427951
|Title=PTPN22.6, a Dominant Negative Isoform of PTPN22 and Potential Biomarker of Rheumatoid Arthritis
|OA=1
}}

{{PMID Auto
|PMID=22396730
|Title=No Association of PTPN22 Polymorphisms with Susceptibility to Ocular Behcet's Disease in Two Chinese Han Populations
|OA=1
}}

{{PMID Auto
|PMID=22632125
|Title=Evidence of cis-acting regulatory variation in PTPN22 in patients with rheumatoid arthritis
}}

{{PMID Auto
|PMID=22696186
|Title=The protein tyrosine phosphatase nonreceptor 22 C1858T polymorphism and vasculitis: a meta-analysis
}}

{{PMID Auto
|PMID=21922340
|Title=Combined influence of genetic and environmental factors in age of rheumatoid arthritis onset.
}}

{{PMID Auto
|PMID=22197427
|Title=PTPN22 and myasthenia gravis: replication in an Italian population and meta-analysis of literature data
}}

{{PMID Auto
|PMID=22743847
|Title=The +1858C/T PTPN22 gene polymorphism confers genetic susceptibility to rheumatoid arthritis in Mexican population from the Western Mexico
}}

{{ClinVar
|rsid=2476601
|Reversed=0
|FwdREF=A
|FwdALT=G
|REF=A
|ALT=G
|RSPOS=113834946
|CHROM=1
|GMAF=0.0421
|dbSNPBuildID=100
|SSR=0
|SAO=1
|VP=0x050168080a0515051f130101
|WGT=1
|VC=SNV
|CLNALLE=0
|CLNHGVS=NC_000001.11:g.113834946A\x3d
|CLNSRC=ClinVar; OMIM Allelic Variant
|CLNORIGIN=1
|CLNSRCID=NM_015967.5:c.1858C>T; 600716.0001
|CLNSIG=255
|CLNCUI=C0003873
|CLNDBN=Diabetes mellitus, insulin-dependent, susceptibility to; Rheumatoid arthritis; Systemic lupus erythematosus, susceptibility to; Hashimoto thyroiditis, susceptibility to; Addison disease, susceptibility to
|Disease=Diabetes mellitus; Rheumatoid arthritis; Systemic lupus erythematosus; Hashimoto thyroiditis; Addison disease
|CLNACC=RCV000009460.1; RCV000009461.1; RCV000009462.1; RCV000009463.1; RCV000009464.1
|Tags=PM;PMC;SLO;NSM;REF;INT;ASP;VLD;G5;HD;GNO;KGPhase1;KGPilot123;KGPROD;OTHERKG;PH3;LSD;MTP;OM
|CAF=0.04224; 0.9578
|CLNDSDB=MedGen:OMIM:SNOMED_CT
|CLNDSDBID=C0003873:180300:69896004
|COMMON=1
|GENEINFO=PTPN22:26191; RP5-1073O3.2:101928822
|GENE_ID=26191; 101928822
|GENE_NAME=PTPN22; RP5-1073O3.2
}}

{{PMID Auto
|PMID=16380915
|Title=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.
|OA=1
}}

{{PMID Auto
|PMID=16464986
|Title=Lack of association between the protein tyrosine phosphatase non-receptor 22 (PTPN22)*620W allele and systemic sclerosis in the French Caucasian population.
|OA=1
}}

{{PMID Auto
|PMID=16945141
|Title=Fine mapping of genes within the IDDM8 region in rheumatoid arthritis.
|OA=1
}}

{{PMID Auto
|PMID=17000021
|Title=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 Auto
|PMID=17044734
|Title=European population substructure: clustering of northern and southern populations.
|OA=1
}}

{{PMID Auto
|PMID=17148556
|Title=Association of PTPN22 haplotypes with Graves' disease.
}}

{{PMID Auto
|PMID=17170052
|Title=Investigation of genetic variation across the protein tyrosine phosphatase gene in patients with rheumatoid arthritis in the UK.
|OA=1
}}

{{PMID Auto
|PMID=17334650
|Title=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.
|OA=1
}}

{{PMID Auto
|PMID=17579671
|Title=Association of PTPN22 single nucleotide polymorphism with rheumatoid arthritis but not with allergic asthma.
}}

{{PMID Auto
|PMID=17606874
|Title=Association of the vitamin D metabolism gene CYP27B1 with type 1 diabetes.
|OA=1
}}

{{PMID Auto
|PMID=17665434
|Title=Association of interleukin-6 and interleukin-10 genotypes with radiographic damage in rheumatoid arthritis is dependent on autoantibody status.
|OA=1
}}

{{PMID Auto
|PMID=17666451
|Title=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.
|OA=1
}}

{{PMID Auto
|PMID=17683561
|Title=The TCF7L2 locus and type 1 diabetes.
|OA=1
}}

{{PMID Auto
|PMID=17868256
|Title=PTPN22 gene polymorphism in Behcet's disease.
}}

{{PMID Auto
|PMID=18075792
|Title=PTPN22: its role in SLE and autoimmunity.
|OA=1
}}

{{PMID Auto
|PMID=18248681
|Title=Prevalence of common disease-associated variants in Asian Indians.
|OA=1
}}

{{PMID Auto
|PMID=18292987
|Title=Joint effects of HLA, INS, PTPN22 and CTLA4 genes on the risk of type 1 diabetes.
|OA=1
}}

{{PMID Auto
|PMID=18310307
|Title=Genetic similarities between latent autoimmune diabetes in adults, type 1 diabetes, and type 2 diabetes.
}}

{{PMID Auto
|PMID=18341666
|Title=Polymorphisms in the PTPN22 region are associated with psoriasis of early onset.
|OA=1
}}

{{PMID Auto
|PMID=18375974
|Title=PTPN22 gene polymorphism in Takayasu's arteritis.
}}

{{PMID Auto
|PMID=18434327
|Title=Re-evaluation of putative rheumatoid arthritis susceptibility genes in the post-genome wide association study era and hypothesis of a key pathway underlying susceptibility.
|OA=1
}}

{{PMID Auto
|PMID=18456185
|Title=Genetics and genomics of primary biliary cirrhosis.
|OA=1
}}

{{PMID Auto
|PMID=18462498
|Title=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.
|OA=1
}}

{{PMID Auto
|PMID=18466461
|Title=Meta-genetic association of rheumatoid arthritis and PTPN22 using PedGenie 2.1.
|OA=1
}}

{{PMID Auto
|PMID=18466472
|Title=Constructing gene association networks for rheumatoid arthritis using the backward genotype-trait association (BGTA) algorithm.
|OA=1
}}

{{PMID Auto
|PMID=18466483
|Title=Modeling of PTPN22 and HLA-DRB1 susceptibility to rheumatoid arthritis.
|OA=1
}}

{{PMID Auto
|PMID=18466513
|Title=Evaluating gene x gene and gene x smoking interaction in rheumatoid arthritis using candidate genes in GAW15.
|OA=1
}}

{{PMID Auto
|PMID=18466529
|Title=Comparing strategies for evaluation of candidate genes in case-control studies using family data.
|OA=1
}}

{{PMID Auto
|PMID=18466531
|Title=Case-control association analysis of rheumatoid arthritis with candidate genes using related cases.
|OA=1
}}

{{PMID Auto
|PMID=18466535
|Title=Modeling the effect of PTPN22 in rheumatoid arthritis.
|OA=1
}}

{{PMID Auto
|PMID=18466554
|Title=Analyses of single marker and pairwise effects of candidate loci for rheumatoid arthritis using logistic regression and random forests.
|OA=1
}}

{{PMID Auto
|PMID=18466563
|Title=Classification of rheumatoid arthritis status with candidate gene and genome-wide single-nucleotide polymorphisms using random forests.
|OA=1
}}

{{PMID Auto
|PMID=18535005
|Title=The search for genes contributing to endometriosis risk.
|OA=1
}}

{{PMID Auto
|PMID=18556337
|Title=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).
|OA=1
}}

{{PMID Auto
|PMID=18648537
|Title=A large-scale rheumatoid arthritis genetic study identifies association at chromosome 9q33.2.
|OA=1
}}

{{PMID Auto
|PMID=18668548
|Title=Genome-wide association study of rheumatoid arthritis in the Spanish population: KLF12 as a risk locus for rheumatoid arthritis susceptibility.
}}

{{PMID Auto
|PMID=18710467
|Title=The tryptophan 620 allele of the lymphoid tyrosine phosphatase (PTPN22) gene predisposes to autoimmune Addison's disease.
}}

{{PMID Auto
|PMID=18759295
|Title=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.
|OA=1
}}

{{PMID Auto
|PMID=18776148
|Title=Joint genetic susceptibility to type 1 diabetes and autoimmune thyroiditis: from epidemiology to mechanisms.
|OA=1
}}

{{PMID Auto
|PMID=18794853
|Title=Common variants at CD40 and other loci confer risk of rheumatoid arthritis.
|OA=1
}}

{{PMID Auto
|PMID=18821667
|Title=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 Auto
|PMID=18978792
|Title=Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci.
|OA=1
}}

{{PMID Auto
|PMID=18987647
|Title=Rheumatoid arthritis: a view of the current genetic landscape.
|OA=1
}}

{{PMID Auto
|PMID=19068216
|Title=Investigation of Crohn's disease risk loci in ulcerative colitis further defines their molecular relationship.
|OA=1
}}

{{PMID Auto
|PMID=19073967
|Title=Shared and distinct genetic variants in type 1 diabetes and celiac disease.
|OA=1
}}

{{PMID Auto
|PMID=19098027
|Title=SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms.
|OA=1
}}

{{PMID Auto
|PMID=19119414
|Title=IL2RA genetic heterogeneity in multiple sclerosis and type 1 diabetes susceptibility and soluble interleukin-2 receptor production.
|OA=1
}}

{{PMID Auto
|PMID=19180256
|Title=Genotype analysis of polymorphisms in autoimmune susceptibility genes, CTLA-4 and PTPN22, in an acute anterior uveitis cohort.
|OA=1
}}

{{PMID Auto
|PMID=19180477
|Title=Genetic risk factors for rheumatoid arthritis differ in Caucasian and Korean populations.
|OA=1
}}

{{PMID Auto
|PMID=19188433
|Title=Do non-HLA genes influence development of persistent islet autoimmunity and type 1 diabetes in children with high-risk HLA-DR,DQ genotypes?
|OA=1
}}

{{PMID Auto
|PMID=19210888
|Title=Role of HLA-DRB1 and PTPN22 genes in susceptibility to juvenile idiopathic arthritis in Hungarian patients.
}}

{{PMID Auto
|PMID=19408013
|Title=Strategies and issues in the detection of pathway enrichment in genome-wide association studies.
|OA=1
}}

{{PMID Auto
|PMID=19445664
|Title=Association of common polymorphisms in known susceptibility genes with rheumatoid arthritis in a Slovak population using osteoarthritis patients as controls.
|OA=1
}}

{{PMID Auto
|PMID=19474294
|Title=Potential etiologic and functional implications of genome-wide association loci for human diseases and traits.
|OA=1
}}

{{PMID Auto
|PMID=19503742
|Title=Evaluation of PTPN22 polymorphisms and Vogt-Koyanagi-Harada disease in Japanese patients.
|OA=1
}}

{{PMID Auto
|PMID=19557189
|Title=Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions.
|OA=1
}}

{{PMID Auto
|PMID=19569043
|Title=Genome-wide association studies and the genetic dissection of complex traits.
|OA=1
}}

{{PMID Auto
|PMID=19591781
|Title=The search for lupus biomarkers.
|OA=1
}}

{{PMID Auto
|PMID=19682379
|Title=TagSNP transferability and relative loss of variability prediction from HapMap to an admixed population.
|OA=1
}}

{{PMID Auto
|PMID=19776214
|Title=SimCT: a generic tool to visualize ontology-based relationships for biological objects.
|OA=1
}}

{{PMID Auto
|PMID=19838195
|Title=A large-scale replication study identifies TNIP1, PRDM1, JAZF1, UHRF1BP1 and IL10 as risk loci for systemic lupus erythematosus.
|OA=1
}}

{{PMID Auto
|PMID=19923204
|Title=Genetic background of systemic sclerosis: autoimmune genes take centre stage.
}}

{{PMID Auto
|PMID=19924720
|Title=Analysis of multiple phenotypes.
|OA=1
}}

{{PMID Auto
|PMID=19956101
|Title=Overview of the Rapid Response data.
|OA=1
}}

{{PMID Auto
|PMID=19956109
|Title=The Type I Diabetes Genetics Consortium 'Rapid Response' family-based candidate gene study: strategy, genes selection, and main outcome.
|OA=1
}}

{{PMID Auto
|PMID=20017963
|Title=Representation of genetic association via attributable familial relative risks in order to identify polymorphisms functionally relevant to rheumatoid arthritis.
|OA=1
}}

{{PMID Auto
|PMID=20017967
|Title=Genome-wide association analyses of North American Rheumatoid Arthritis Consortium and Framingham Heart Study data utilizing genome-wide linkage results.
|OA=1
}}

{{PMID Auto
|PMID=20017974
|Title=Simultaneous analysis of all single-nucleotide polymorphisms in genome-wide association study of rheumatoid arthritis.
|OA=1
}}

{{PMID Auto
|PMID=20017985
|Title=Adjusting for HLA-DRbeta1 in a genome-wide association analysis of rheumatoid arthritis and related biomarkers.
|OA=1
}}

{{PMID Auto
|PMID=20017996
|Title=Effect of population stratification on the identification of significant single-nucleotide polymorphisms in genome-wide association studies.
|OA=1
}}

{{PMID Auto
|PMID=20018006
|Title=Case-control genome-wide association study of rheumatoid arthritis from Genetic Analysis Workshop 16 using penalized orthogonal-components regression-linear discriminant analysis.
|OA=1
}}

{{PMID Auto
|PMID=20018016
|Title=Application of seventeen two-locus models in genome-wide association studies by two-stage strategy.
|OA=1
}}

{{PMID Auto
|PMID=20018019
|Title=Two-stage joint selection method to identify candidate markers from genome-wide association studies.
|OA=1
}}

{{PMID Auto
|PMID=20018022
|Title=Replication of recently identified associated single-nucleotide polymorphisms from six autoimmune diseases in Genetic Analysis Workshop 16 rheumatoid arthritis data.
|OA=1
}}

{{PMID Auto
|PMID=20018025
|Title=Genome-wide analysis of haplotype interaction for the data from the North American Rheumatoid Arthritis Consortium.
|OA=1
}}

{{PMID Auto
|PMID=20018027
|Title=Conditional analysis of the major histocompatibility complex in rheumatoid arthritis.
|OA=1
}}

{{PMID Auto
|PMID=20018035
|Title=A combinatorial approach for detecting gene-gene interaction using multiple traits of Genetic Analysis Workshop 16 rheumatoid arthritis data.
|OA=1
}}

{{PMID Auto
|PMID=20018042
|Title=Assessment of genotype imputation methods.
|OA=1
}}

{{PMID Auto
|PMID=20018049
|Title=Evaluation of an optimal receiver operating characteristic procedure.
|OA=1
}}

{{PMID Auto
|PMID=20018053
|Title=A genome-wide association scan for rheumatoid arthritis data by Hotelling's T2 tests.
|OA=1
}}

{{PMID Auto
|PMID=20018054
|Title=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.
|OA=1
}}

{{PMID Auto
|PMID=20018057
|Title=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.
|OA=1
}}

{{PMID Auto
|PMID=20018062
|Title=Identification of genes and haplotypes that predict rheumatoid arthritis using random forests.
|OA=1
}}

{{PMID Auto
|PMID=20018071
|Title=Allelic based gene-gene interactions in rheumatoid arthritis.
|OA=1
}}

{{PMID Auto
|PMID=20018074
|Title=Identifying rheumatoid arthritis susceptibility genes using high-dimensional methods.
|OA=1
}}

{{PMID Auto
|PMID=20018080
|Title=Effects of covariates and interactions on a genome-wide association analysis of rheumatoid arthritis.
|OA=1
}}

{{PMID Auto
|PMID=20018090
|Title=Comparative analysis of different approaches for dealing with candidate regions in the context of a genome-wide association study.
|OA=1
}}

{{PMID Auto
|PMID=20089178
|Title=Allelic variants in the PHTF1-PTPN22, C12orf30 and CD226 regions as candidate susceptibility factors for the type 1 diabetes in the Estonian population.
|OA=1
}}

{{PMID Auto
|PMID=20166877
|Title=Allele and haplotype frequency distribution in PTPN22 gene across variable ethnic groups: Implications for genetic association studies for autoimmune diseases.
}}

{{PMID Auto
|PMID=20236493
|Title=The contribution of genetic variation and infection to the pathogenesis of ANCA-associated systemic vasculitis.
|OA=1
}}

{{PMID Auto
|PMID=20353580
|Title=Evaluation of the rheumatoid arthritis susceptibility loci HLA-DRB1, PTPN22, OLIG3/TNFAIP3, STAT4 and TRAF1/C5 in an inception cohort.
|OA=1
}}

{{PMID Auto
|PMID=20403149
|Title=PTPN2 but not PTPN22 is associated with Crohn's disease in a New Zealand population.
}}

{{PMID Auto
|PMID=20439292
|Title=Genetic variants in the prediction of rheumatoid arthritis.
}}

{{PMID Auto
|PMID=20444268
|Title=Peripheral blood gene expression patterns discriminate among chronic inflammatory diseases and healthy controls and identify novel targets.
|OA=1
}}

{{PMID Auto
|PMID=20696024
|Title=PTPN22 polymorphism is related to autoimmune disease risk in patients with Turner syndrome.
}}

{{PMID Auto
|PMID=20722033
|Title=The susceptibility loci juvenile idiopathic arthritis shares with other autoimmune diseases extend to PTPN2, COG6, and ANGPT1.
|OA=1
}}

{{PMID Auto
|PMID=21078766
|Title=The association between the PTPN22 C1858T polymorphism and systemic lupus erythematosus: a meta-analysis update.
}}

{{PMID Auto
|PMID=21193990
|Title=A PTPN22 promoter polymorphism -1123G>C is associated with RA pathogenesis in Chinese.
}}

{{PMID Auto
|PMID=21304977
|Title=An investigation of genome-wide studies reported susceptibility loci for ulcerative colitis shows limited replication in north Indians.
|OA=1
}}

{{PMID Auto
|PMID=21379322
|Title=Risk alleles for systemic lupus erythematosus in a large case-control collection and associations with clinical subphenotypes.
|OA=1
}}

{{PMID Auto
|PMID=21383967
|Title=Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci.
|OA=1
}}

{{PMID Auto
|PMID=21408207
|Title=Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production.
|OA=1
}}

{{PMID Auto
|PMID=21506938
|Title=Association of the PTPN22 gene polymorphism with autoantibody positivity in Turkish rheumatoid arthritis patients.
}}

{{PMID Auto
|PMID=21570397
|Title=Susceptibility to amoxicillin-clavulanate-induced liver injury is influenced by multiple HLA class I and II alleles.
|OA=1
}}

{{PMID Auto
|PMID=21752868
|Title=PTPN22 R620W genotype-phenotype correlation analysis and gene-environment interaction study in early rheumatoid arthritis: results from the ESPOIR cohort.
}}

{{PMID Auto
|PMID=22210423
|Title=Lack of association of the rs2476601 PTPN22 gene polymorphism with transplanted kidney function.
}}

{{PMID Auto
|PMID=22327470
|Title=The association between the functional PTPN22 1858 C/T and MIF -173 C/G polymorphisms and juvenile idiopathic arthritis: a meta-analysis.
}}

{{PMID Auto
|PMID=22493691
|Title=Novel associations for hypothyroidism include known autoimmune risk loci.
|OA=1
}}

{{PMID Auto
|PMID=22511809
|Title=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 Auto
|PMID=22544573
|Title=PTPN22 C1858T and the risk of psoriasis: a meta-analysis.
}}

{{GET Evidence
|gene=PTPN22
|aa_change=Trp565Arg
|aa_change_short=W565R
|impact=not reviewed
|qualified_impact=Insufficiently evaluated not reviewed
|inheritance=unknown
|quality_scores=Array
|dbsnp_id=rs2476601
|n_genomes=1
|n_genomes_annotated=0
|n_haplomes=1
|n_articles=0
|n_articles_annotated=0
|nblosum100=7
|autoscore=1
|webscore=N
}}

[[Hashimoto's Thyroiditis]]

{{PMID Auto GWAS
  |PMID=23055271
  |Trait=Myasthenia gravis
  |Title=Risk for myasthenia gravis maps to a (151) Pro→Ala change in TNIP1 and to human leukocyte antigen-B*08.
  |RiskAllele=A
  |Pval=8E-10
  |OR=1.71
  |ORtxt=[1.44-2.02]
  |OA=1
}}

{{PMID Auto GWAS
  |PMID=21102463
  |Trait=Crohn's disease
  |Title=Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
  |RiskAllele=G
  |Pval=4E-9
  |OR=1.26
  |ORtxt=[1.17-1.37]
  |OA=1
}}

{{PMID Auto
|PMID=23946333
|Title=Identification of the PTPN22 functional variant R620W as susceptibility genetic factor for giant cell arteritis
}}

{{PMID Auto
|PMID=23944755
|Title=The impact of CTLA4 and PTPN22 genes polymorphisms on long-term renal allograft function and transplant outcomes
}}

{{PMID Auto
|PMID=23950893
|Title=PTPN22 Association in Systemic Lupus Erythematosus (SLE) with Respect to Individual Ancestry and Clinical Sub-Phenotypes
|OA=1
}}

{{PMID Auto
|PMID=23974994
|Title=Replication Study of Ulcerative Colitis Risk Loci in a Lithuanian-Latvian Case-Control Sample
}}

{{PMID Auto
|PMID=24160187
|Title=Meta-analysis confirms association between TNFA-G238A variant and JIA, and between PTPN22-C1858T variant and oligoarticular, RF-polyarticular and RF-positive polyarticular JIA
|OA=1
}}

{{PMID Auto
|PMID=23582631
|Title=Pathway analysis of genome-wide association studies on rheumatoid arthritis
}}

{{PMID Auto
|PMID=24386393
|Title=Genetic Heterogeneity of Susceptibility Gene in Different Ethnic Populations: Refining Association Study of PTPN22 for Graves' Disease in a Chinese Han Population
|OA=1
}}

{{PMID Auto
|PMID=24103478
|Title=Contribution of PTPN22, CD28, CTLA-4 and ZAP-70 variants to the risk of type 1 diabetes in Tunisians
}}

{{PMID Auto
|PMID=22328738
|Title=Comprehensive assessment of rheumatoid arthritis susceptibility loci in a large psoriatic arthritis cohort.
|OA=1
}}

{{PMID Auto
|PMID=22440825
|Title=Relationship between area-level socio-economic deprivation and autoantibody status in patients with rheumatoid arthritis: multicentre cross-sectional study.
}}

{{PMID Auto
|PMID=22674012
|Title=Association of anti-citrullinated vimentin and anti-citrullinated alpha-enolase antibodies with subsets of rheumatoid arthritis.
}}

{{PMID Auto
|PMID=22857794
|Title=Autoimmunity in primary antibody deficiency is associated with protein tyrosine phosphatase nonreceptor type 22 (PTPN22).
}}

{{PMID Auto
|PMID=23054006
|Title=Meta-analysis of the family-based association between the PTPN22 C1858T polymorphism and type 1 diabetes.
}}

{{PMID Auto
|PMID=23223422
|Title=Identification of the NF-kappaB activating protein-like locus as a risk locus for rheumatoid arthritis.
|OA=1
}}

{{PMID Auto
|PMID=23350658
|Title=Association of PTPN22 rs2476601 and EGFR rs17337023 Gene polymorphisms and rheumatoid arthritis in Zahedan, Southeast Iran.
}}

{{PMID Auto
|PMID=23450725
|Title=Susceptibility to childhood-onset rheumatoid arthritis: investigation of a weighted genetic risk score that integrates cumulative effects of variants at five genetic loci.
}}

{{PMID Auto
|PMID=23463390
|Title=Variants in PTPN22 and SMOC2 genes and the risk of thyroid disease in the Jordanian Arab population.
}}

{{PMID Auto
|PMID=23637320
|Title=Metaanalysis of the association of smoking and PTPN22 R620W genotype on autoantibody status and radiological erosions in rheumatoid arthritis.
}}

{{PMID Auto
|PMID=23777930
|Title=Investigation of juvenile idiopathic arthritis susceptibility loci: results from a Greek population.
}}

{{PMID Auto
|PMID=24880676
|Title=Protein tyrosine phosphatase non-receptor type 22 (PTPN22) +1858 C&gt;T gene polymorphism in Egyptian cases with rheumatoid arthritis
}}

{{PMID Auto
|PMID=24913133
|Title=Association of PTPN22+1858C/T polymorphism with Type 1 diabetes in the North Indian population
}}

{{PMID Auto
|PMID=24971461
|Title=Polymorphisms in the Inflammatory Pathway Genes TLR2, TLR4, TLR9, LY96, NFKBIA, NFKB1, TNFA, TNFRSF1A, IL6R, IL10, IL23R, PTPN22, and PPARG Are Associated with Susceptibility of Inflammatory Bowel Disease in a Danish Cohort
}}

{{PMID Auto
|PMID=25003765
|Title=PTPN22: the archetypal non-HLA autoimmunity gene
}}

{{PMID Auto
|PMID=25005490
|Title=The association of PTPN22 rs2476601 polymorphism and CTLA-4 rs231775 polymorphism with LADA risks: a systematic review and meta-analysis
}}

{{PMID Auto
|PMID=25073032
|Title=Association Between a Gain-of-Function Variant of PTPN22 and Rejection in Liver Transplantation
}}

{{PMID Auto GWAS
  |PMID=24390342
  |Trait=Rheumatoid arthritis
  |Title=Genetics of rheumatoid arthritis contributes to biology and drug discovery.
  |RiskAllele=A
  |Pval=9E-170
  |OR=1.80
  |ORtxt=[1.73-1.88]
  }}

{{PMID Auto
|PMID=25138370
|Title=Non-HLA genes PTPN22, CDK6 and PADI4 are associated with specific autoantibodies in HLA-defined subgroups of rheumatoid arthritis
}}
{{on chip | 23andMe v1}}
{{on chip | 23andMe v2}}
{{on chip | 23andMe v3}}
{{on chip | 23andMe v4}}
{{on chip | HumanOmni1Quad}}
{{on chip | Illumina Human 1M}}