rs2542151

A SNP in the PTPN2 gene on chromosome 18. Its most notable genotype is G;G: 2x risk for Crohn's; 1.6x for T1D

Gene
PTPN2
Location
Chr 1812,779,948 (GRCh38)
Highest magnitude
2.0Worth knowing
Tested on
23andMe, AncestryDNA
Minor allele frequency
16%

Genotypes

As shown in 23andMe and AncestryDNA files.

  1. G;GMost notableBad2x risk for Crohn's; 1.6x for T1DWorth knowing · 2.02% of people
  2. G;TBad1.3x risk for Crohn's; 1.3x for T1DMinor · 1.324% of people
  3. T;TGoodnormalTypical · 0.074% of people

On SNPedia: (G;G), (G;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% G;T 24% T;T 74%
  • European ancestry (Utah)G;G 3% G;T 18% T;T 80%
  • Han Chinese (Beijing)G;G 2% G;T 27% T;T 71%
  • Japanese (Tokyo)G;G 2% G;T 19% T;T 80%
  • Yoruba (Nigeria)G;G 3% G;T 37% T;T 60%
  • African ancestry (Southwest US)G;G 2% G;T 37% T;T 61%
  • Chinese (Denver)G;G <1% G;T 31% T;T 68%
  • Gujarati IndianG;G 2% G;T 18% T;T 80%
  • Luhya (Kenya)G;G 3% G;T 23% T;T 74%
  • Mexican ancestry (Los Angeles)G;G 3% G;T 17% T;T 79%
  • Maasai (Kenya)G;G 3% G;T 17% T;T 81%
  • TuscanG;G 2% G;T 19% T;T 79%

Conditions, medicines and genes

Other PTPN2 SNPs

All PTPN2 SNPs

Notes

From SNPedia

Notes

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). 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). 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 1.22&#226;&#8364;&#8220;1.40).

Source and license

Adapted from rs2542151 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 Its entries can be incomplete, out of date or wrong, and nothing here is a diagnosis or medical advice.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.