{{Rsnum
|rsid=1893217
|Gene=PTPN2
|Chromosome=18
|position=12809341
|Orientation=minus
|GMAF=0.118
|Assembly=GRCh38
|GenomeBuild=38.1
|dbSNPBuild=141
|geno1=(C;C)
|geno2=(C;T)
|geno3=(T;T)
|Gene_s=PTPN2
}}{{ population diversity
| geno1=(C;C)
| geno2=(C;T)
| geno3=(T;T)
| CEU | 2.7 | 17.7 | 79.6
| HCB | 2.9 | 27.0 | 70.1
| JPT | 1.8 | 17.7 | 80.5
| YRI | 0.7 | 9.5 | 89.8
| ASW | 0.0 | 8.8 | 91.2
| CHB | 2.9 | 27.0 | 70.1
| CHD | 0.9 | 33.9 | 65.1
| GIH | 2.0 | 18.8 | 79.2
| LWK | 0.0 | 10.0 | 90.0
| MEX | 3.4 | 10.3 | 86.2
| MKK | 2.6 | 12.3 | 85.2
| TSI | 1.0 | 19.6 | 79.4
| HapMapRevision=28
}}

linked to [[Crohn's disease]] and [[type-1 diabetes]]

{{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=4E-15
|OR=NR
|ORtxt=NR
|OA=1
}}

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

{{PMID Auto
|PMID=20222910
|Title=Susceptibility loci reported in genome-wide association studies are associated with Crohn's disease in Canadian children
}}
{{PMID Auto GWAS
|PMID=20190752
|Trait=Celiac disease
|Title=Multiple common variants for celiac disease influencing immune gene expression
|RiskAllele=G
|Pval=3E-10
|OR=1.17
|ORtxt=[1.12-1.23]
|OA=1
}}
{{PMID Auto
|PMID=21179116
|Title=An autoimmune-associated variant in PTPN2 reveals an impairment of IL-2R signaling in CD4(+) T cells
|OA=1
}}

{{PMID Auto GWAS
|PMID=21383967
|Trait=None
|Title=Meta-Analysis of Genome-Wide Association Studies in Celiac Disease and Rheumatoid Arthritis Identifies Fourteen Non-HLA Shared Loci
|RiskAllele=G
|Pval=5E-12
|OR=None
|ORtxt=None
|OA=1
}}

{{PMID|17554260|OA=1
}} Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes.

{{PMID|18252225|OA=1
}} On the use of general control samples for genome-wide association studies: genetic matching highlights causal variants.

{{PMID|18556337|OA=1
}} 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|18987646|OA=1
}} The expanding genetic overlap between multiple sclerosis and type I diabetes.

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

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

{{PMID|22021207}} Crohn's disease-associated polymorphism within the PTPN2 gene affects muramyl-dipeptide-induced cytokine secretion and autophagy.

{{GET Evidence
|impact=pathogenic
|qualified_impact=Insufficiently evaluated pathogenic
|inheritance=unknown
|quality_scores=Array
|dbsnp_id=rs1893217
|overall_frequency_n=10
|overall_frequency_d=128
|overall_frequency=0.078125
|n_genomes=9
|n_genomes_annotated=0
|n_haplomes=9
|n_articles=0
|n_articles_annotated=0
|in_gwas=Y
|autoscore=1
|webscore=N
}}

{{PMID Auto GWAS
  |PMID=23128233
  |Trait=Inflammatory bowel disease
  |Title=Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
  |RiskAllele=G
  |Pval=3E-26
  |OR=1.17
  |ORtxt=[1.127-1.216]
  |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=1E-14
  |OR=1.25
  |ORtxt=[1.18-1.32]
  |OA=1
}}

{{PMID Auto
|PMID=24127071
|Title=Associations between PTPN2 polymorphisms and susceptibility to ulcerative colitis and Crohn's disease: a meta-analysis
}}

{{PMID Auto
|PMID=23518806
|Title=Association between the PTPN2 gene and Crohn's disease: dissection of potential causal variants
}}

{{PMID Auto
|PMID=24480412
|Title=PTPN2 rs1893217 single-nucleotide polymorphism is associated with risk of Behçet's disease in a Chinese Han population
}}

{{PMID Auto
|PMID=22960018
|Title=Investigation of the vitamin D receptor gene (VDR) and its interaction with protein tyrosine phosphatase, non-receptor type 2 gene (PTPN2) on risk of islet autoimmunity and type 1 diabetes: the Diabetes Autoimmunity Study in the Young (DAISY).
|OA=1
}}

{{on chip | 23andMe v1}}
{{on chip | 23andMe v2}}
{{on chip | 23andMe v3}}
{{on chip | 23andMe v4}}
{{on chip | HumanOmni1Quad}}
{{on chip | Illumina Human 1M}}