rs2488457

A SNP in the PTPN22 gene on chromosome 1. Its most notable genotype is C;C: Slightly increased (~1.7x) risk for certain autoimmune diseases in some populations

Gene
PTPN22
Location
Chr 1113,872,746 (GRCh38)
Highest magnitude
1.7Minor
Tested on
23andMe, AncestryDNA
Minor allele frequency
29%

Genotypes

Plus strand, as in 23andMe and AncestryDNA files.

  1. G;GGoodcommon/normalTypical · 0.014% of people
  2. C;GBadSlightly increased (~1.5x) risk for certain autoimmune diseases in some populationsMinor · 1.528% of people
  3. C;CMost notableBadSlightly increased (~1.7x) risk for certain autoimmune diseases in some populationsMinor · 1.759% of people

SNPedia records rs2488457 on the minus strand: (C;C), (C;G), (G;G). 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 14% C;G 28% C;C 59%
  • European ancestry (Utah)G;G 7% C;G 29% C;C 64%
  • Han Chinese (Beijing)G;G 42% C;G 47% C;C 11%
  • Japanese (Tokyo)G;G 30% C;G 50% C;C 20%
  • Yoruba (Nigeria)G;G 0% C;G 0% C;C 100%
  • African ancestry (Southwest US)G;G 2% C;G 5% C;C 93%
  • Chinese (Denver)G;G 44% C;G 48% C;C 8%
  • Gujarati IndianG;G 6% C;G 32% C;C 62%
  • Luhya (Kenya)G;G 0% C;G 4% C;C 96%
  • Mexican ancestry (Los Angeles)G;G 14% C;G 41% C;C 45%
  • Maasai (Kenya)G;G 0% C;G 14% C;C 87%
  • TuscanG;G 5% C;G 34% C;C 61%

Conditions, medicines and genes

Other PTPN22 SNPs

All PTPN22 SNPs

Notes

From SNPedia

Show notes, about 300 words

rs2488457, known in the literature as c.-1123C>G, represents a variant in the upstream promoter region of the PTPN22 gene on chromosome 1. In at least some studies and in some populations, the minor allele is linked to slightly increased risk for autoimmune diseases such as Crohn's disease, type-1 diabetes, multiple sclerosis, rheumatoid arthritis, lupus, and celiac disease. 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. Further evidence of a primary, causal association of the PTPN22 620W variant with type 1 diabetes. PTPN22: its role in SLE and autoimmunity. On the use of general control samples for genome-wide association studies: genetic matching highlights causal variants. Associations of protein tyrosine phosphatase nonreceptor 22 (PTPN22) gene polymorphisms with susceptibility to Graves' disease in a Japanese population. Genetic risk factors for rheumatoid arthritis differ in Caucasian and Korean populations. rs2476601 T allele (R620W) defines high-risk PTPN22 type I diabetes-associated haplotypes with preliminary evidence for an additional protective haplotype. Overview of the Rapid Response data. Analysis of 19 genes for association with type I diabetes in the Type I Diabetes Genetics Consortium families. The susceptibility loci juvenile idiopathic arthritis shares with other autoimmune diseases extend to PTPN2, COG6, and ANGPT1. A PTPN22 promoter polymorphism -1123G>C is associated with RA pathogenesis in Chinese. No association of PTPN22 polymorphisms with susceptibility to ocular Behcet's disease in two Chinese Han populations.

C;G

see discussion and citations via main rs-page

C;C

See discussion and citations via main rs-page

Source and license

Adapted from rs2488457 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.