rs1893217

A SNP in the PTPN2 gene on chromosome 18. Its most notable genotype is G;G: Somewhat increased (~2x) risk for Crohn's disease

Gene
PTPN2
Location
Chr 1812,809,341 (GRCh38)
Highest magnitude
2.0Worth knowing
Tested on
23andMe, AncestryDNA
Minor allele frequency
12%

Genotypes

Plus strand, as in 23andMe and AncestryDNA files.

  1. G;GMost notableBadSomewhat increased (~2x) risk for Crohn's diseaseWorth knowing · 2.02% of people
  2. A;GBadSlightly increased (1.4x) risk for Crohn's diseaseMinor · 1.417% of people
  3. A;AGoodcommon/normalTypical · 0.081% of people

SNPedia records rs1893217 on the minus strand: (C;C), (C;T), (T;T). Magnitude rates how notable a genotype is from 0 to 10, not how risky it is.

Frequency

Share of each genotype in 11 HapMap populations.

  • AverageG;G 2% A;G 17% A;A 81%
  • European ancestry (Utah)G;G 3% A;G 18% A;A 80%
  • Han Chinese (Beijing)G;G 3% A;G 27% A;A 70%
  • Japanese (Tokyo)G;G 2% A;G 18% A;A 81%
  • Yoruba (Nigeria)G;G <1% A;G 10% A;A 90%
  • African ancestry (Southwest US)G;G 0% A;G 9% A;A 91%
  • Chinese (Denver)G;G <1% A;G 34% A;A 65%
  • Gujarati IndianG;G 2% A;G 19% A;A 79%
  • Luhya (Kenya)G;G 0% A;G 10% A;A 90%
  • Mexican ancestry (Los Angeles)G;G 3% A;G 10% A;A 86%
  • Maasai (Kenya)G;G 3% A;G 12% A;A 85%
  • TuscanG;G 1% A;G 20% A;A 79%

Conditions, medicines and genes

Other PTPN2 SNPs

All PTPN2 SNPs

Notes

From SNPedia

Show notes, about 140 words

linked to Crohn's disease and type-1 diabetes Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes. On the use of general control samples for genome-wide association studies: genetic matching highlights causal variants. 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). The expanding genetic overlap between multiple sclerosis and type I diabetes. Shared and distinct genetic variants in type 1 diabetes and celiac disease. The susceptibility loci juvenile idiopathic arthritis shares with other autoimmune diseases extend to PTPN2, COG6, and ANGPT1. Crohn's disease-associated polymorphism within the PTPN2 gene affects muramyl-dipeptide-induced cytokine secretion and autophagy.

Source and license

Adapted from rs1893217 on SNPedia, using a snapshot taken October 16, 2026. SNPedia content is shared under CC BY-NC-SA 3.0 US, and this page is shared under the same license.

SNPedia is a community-edited wiki. Its entries can be incomplete, out of date or wrong, and nothing here is a diagnosis or medical advice. Magnitude is a community rating of how interesting a genotype is, not a risk score.