{{Rsnum
|rsid=2542151
|Gene=PTPN2
|Chromosome=18
|position=12779948
|Orientation=plus
|GMAF=0.1561
|Assembly=GRCh38
|GenomeBuild=38.1
|dbSNPBuild=141
|geno1=(G;G)
|geno2=(G;T)
|geno3=(T;T)
}}{{ population diversity
| geno1=(G;G)
| geno2=(G;T)
| geno3=(T;T)
| CEU | 2.7 | 17.7 | 79.6
| HCB | 2.2 | 26.5 | 71.3
| JPT | 1.8 | 18.6 | 79.6
| YRI | 3.4 | 37.0 | 59.6
| ASW | 1.8 | 36.8 | 61.4
| CHB | 2.2 | 26.5 | 71.3
| CHD | 0.9 | 31.1 | 67.9
| GIH | 2.0 | 17.8 | 80.2
| LWK | 2.8 | 22.9 | 74.3
| MEX | 3.4 | 17.2 | 79.3
| MKK | 2.6 | 16.7 | 80.8
| TSI | 2.0 | 18.6 | 79.4
| HapMapRevision=28
}}[[rs2542151]] has been reported in a large study to be associated with [[Crohn's disease]].
The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.3 (CI 1.14-1.48), and for homozygotes, 2.01 (CI 1.46-2.76). {{PMID|17554300|OA=1
}}

[[rs2542151]] has been reported in the same study to be associated with [[type-1 diabetes]]. 
The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.30 (CI 1.15-1.47), and for homozygotes, 1.62 (CI 1.17-2.24). {{PMID|17554300|OA=1
}}

In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for this SNP was recalculated to be 1.30 (CI 1.22â€“1.40). {{PMID|17554260|OA=1
}}

{{GWAS Summary
|SNP=rs2542151
|PubMedID=17554260
|Condition=Type 1 diabetes
|Gene=PTPN2
|Risk Allele=C
|pValue=1.00E-014
|OR=1.3
|95CI=1.22-1.40
|OA=1
}}

{{PMID Auto GWAS
|PMID=18978792
|Trait=Type 1 diabetes
|Title=Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci
|RiskAllele=C
|Pval=9E-8
|OR=NR
|ORtxt=NR
|OA=1
}}
{{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=4.9999999999999999E-17
|OR=1.35
|ORtxt=[NR]
|OA=1
}}
{{PMID Auto GWAS
|PMID=17554261
|Trait=Crohn's disease
|Title=Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility
|RiskAllele=
|Pval=2.9999999999999997E-8
|OR=1.15
|ORtxt=[1.00-1.32]
|OA=1
}}
{{PMID Auto
|PMID=19565500
|Title=Variants in TNFAIP3, STAT4, and C12orf30 loci associated with multiple autoimmune diseases are also associated with juvenile idiopathic arthritis
|OA=1
}}

{{omim
|desc=INFLAMMATORY BOWEL DISEASE 21; IBD21
|id=612354
|rsnum=2542151
}}

{{omim
|desc=DIABETES MELLITUS, INSULIN-DEPENDENT; IDDM
|id=222100
|rsnum=2542151
}}

{{PharmGKB
|RSID=rs2542151
|Name_s=
|Gene_s=-
|Feature=
|Evidence=PubMed ID:18978792; Web Resource:http://www.genome.gov/gwastudies/
|Annotation=GWAS results: Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci. (Initial Sample Size: 3,561 cases, 4,646 controls; Replication Sample Size: 6,225 cases, 6,946 controls, 3,064 trios); (Region: 18p11.21; Reported Gene(s): PTPN2; Risk Allele: rs2542151-C); (p-value= 0.00000009).This variant is associated with Type 1 diabetes.
|Drugs=
|Drug Classes=
|Diseases=Diabetes Mellitus; Diabetes Mellitus, Type 1
|Curation Level=Non-Curated
|PharmGKB Accession ID=PA164740753
}}

{{PMID Auto
|PMID=19953089
|Title=Differences in genetic background between active smokers, passive smokers, and non-smokers with Crohn's disease
}}

{{PharmGKB
|RSID=rs2542151
|Name_s=
|Gene_s=-
|Feature=
|Evidence=PubMed ID:17554260; Web Resource:http://www.genome.gov/gwastudies/
|Annotation=GWAS Results: Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes (Initial Sample Size: 1,963 cases, 2,938 controls; Replication Sample Size: 4,000 cases, 5,000 controls, 2,997 trios; Risk Allele: rs2542151-C).
|Drugs=
|Drug Classes=
|Diseases=Diabetes Mellitus; Diabetes Mellitus, Type 1
|Curation Level=Non-Curated
|PharmGKB Accession ID=PA162356633
}}

{{PharmGKB
|RSID=rs2542151
|Name_s=
|Gene_s=-
|Feature=
|Evidence=PubMed ID:17554300; Web Resource:http://www.genome.gov/gwastudies/
|Annotation=GWAS Results: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Initial Sample Size: 1,748 cases, 2,938 controls; Replication Sample Size: (see Parkes 2007); Risk Allele: rs2542151-G). This variant is associated with crohn's disease.
|Drugs=
|Drug Classes=
|Diseases=Crohn Disease
|Curation Level=Non-Curated
|PharmGKB Accession ID=PA162356648
}}

{{PharmGKB
|RSID=rs2542151
|Name_s=
|Gene_s=-
|Feature=
|Evidence=PubMed ID:17554261; Web Resource:http://www.genome.gov/gwastudies/
|Annotation=GWAS results: Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility (Initial Sample Size: 1,748 cases, 2,938 controls; Replication Sample Size: 1,182 cases, 2,024 controls). This variant is associated with Crohn's disease.
|Drugs=
|Drug Classes=
|Diseases=Crohn Disease
|Curation Level=Non-Curated
|PharmGKB Accession ID=PA162356574
}}
{{PMID Auto
|PMID=21246196
|Title=A polymorphism in PTPN2 gene is associated with an earlier onset of type 1 diabetes
}}

{{PMID Auto GWAS
|PMID=21829393
|Trait=None
|Title=Genome-wide association analysis of autoantibody positivity in type 1 diabetes cases.
|RiskAllele=G
|Pval=4E-13
|OR=1.3000
|ORtxt=[NR]
|OA=1
}}

{{PMID Auto
|PMID=22377701
|Title=PTPN2 is associated with Crohn's disease and its expression is regulated by NKX2-3.
|OA=1
}}

{{PMID Auto
|PMID=18224312
|Title=Pharmacogenetics: data, concepts and tools to improve drug discovery and drug treatment.
|OA=1
}}

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

{{PMID Auto
|PMID=18423522
|Title=Estimating odds ratios in genome scans: an approximate conditional likelihood approach.
|OA=1
}}

{{PMID Auto
|PMID=18438406
|Title=Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn's disease.
|OA=1
}}

{{PMID Auto
|PMID=18533027
|Title=Worldwide population differentiation at disease-associated SNPs.
|OA=1
}}

{{PMID Auto
|PMID=18853133
|Title=Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes.
|OA=1
}}

{{PMID Auto
|PMID=19140132
|Title=Unbiased estimation of odds ratios: combining genomewide association scans with replication studies.
|OA=1
}}

{{PMID Auto
|PMID=19359276
|Title=Identification of AF4/FMR2 family, member 3 (AFF3) as a novel rheumatoid arthritis susceptibility locus and confirmation of two further pan-autoimmune susceptibility genes.
|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=19639606
|Title=Correcting "winner's curse" in odds ratios from genomewide association findings for major complex human diseases.
|OA=1
}}

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

{{PMID Auto
|PMID=19915572
|Title=Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region.
|OA=1
}}

{{PMID Auto
|PMID=20369022
|Title=Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations.
|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=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=22021207
|Title=Crohn's disease-associated polymorphism within the PTPN2 gene affects muramyl-dipeptide-induced cytokine secretion and autophagy.
}}

{{PMID Auto
|PMID=22426692
|Title=Confirmation of three inflammatory bowel disease susceptibility loci in a Chinese cohort.
}}

{{GET Evidence
|impact=pathogenic
|qualified_impact=Insufficiently evaluated pathogenic
|inheritance=unknown
|quality_scores=Array
|dbsnp_id=rs2542151
|overall_frequency_n=115
|overall_frequency_d=128
|overall_frequency=0.898438
|n_genomes=55
|n_genomes_annotated=0
|n_haplomes=98
|n_articles=2
|n_articles_annotated=2
|in_gwas=Y
|in_pharmgkb=Y
|autoscore=2
|webscore=N
}}

{{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
}}
{{on chip | 23andMe v2}}
{{on chip | 23andMe v3}}
{{on chip | 23andMe v4}}
{{on chip | Affy GenomeWide 6}}
{{on chip | Illumina Human 1M}}