rs12722489

A SNP in the IL2RA gene on chromosome 10. Its most notable genotype is C;T: a slight increase in risk of developing multiple sclerosis

Gene
IL2RA
Location
Chr 106,060,049 (GRCh38)
Highest magnitude
0.0Typical
Tested on
23andMe, AncestryDNA
Minor allele frequency
10%

Genotypes

Plus strand, as in 23andMe and AncestryDNA files.

  1. C;TMost notableBada slight increase in risk of developing multiple sclerosisTypical · 0.014% of people
  2. C;CBada slight increase in risk of developing multiple sclerosisTypical · 0.085% of people

SNPedia records rs12722489 on the minus strand: (A;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.

  • AverageC;T 14% C;C 85%
  • European ancestry (Utah)C;T 29% C;C 68%
  • Han Chinese (Beijing)C;T 23% C;C 75%
  • Japanese (Tokyo)C;T 21% C;C 77%
  • Yoruba (Nigeria)C;T 0% C;C 100%
  • African ancestry (Southwest US)C;T 5% C;C 93%
  • Chinese (Denver)C;T 23% C;C 75%
  • Gujarati IndianC;T 19% C;C 80%
  • Luhya (Kenya)C;T <1% C;C 99%
  • Mexican ancestry (Los Angeles)C;T 9% C;C 91%
  • Maasai (Kenya)C;T 3% C;C 97%
  • TuscanC;T 21% C;C 76%

Conditions, medicines and genes

Other IL2RA SNPs

All IL2RA SNPs

Notes

From SNPedia

Show notes, about 250 words

The (G) allele of rs12722489, located in the first intron of the IL2RA gene, is associated with a slight increase (25%) in risk of developing multiple sclerosis. [PMID tbd; NEJM 357, 29 July 2007, DA Hafler et al.] Note that the (G) allele is the most common at this position in all known populations. blog post giving perspective on the significance of this snp plos rs12722489 and rs2104286 influence multiple sclerosis and type-1 diabetes Haplotypic analysis of Wellcome Trust Case Control Consortium data. IL2RA and IL7RA genes confer susceptibility for multiple sclerosis in two independent European populations. The complex genetics of multiple sclerosis: pitfalls and prospects. Refining genetic associations in multiple sclerosis. IL2RA genetic heterogeneity in multiple sclerosis and type 1 diabetes susceptibility and soluble interleukin-2 receptor production. IL2RA/CD25 gene polymorphisms: uneven association with multiple sclerosis (MS) and type 1 diabetes (T1D). Soluble IL-2RA levels in multiple sclerosis subjects and the effect of soluble IL-2RA on immune responses. Comprehensive follow-up of the first genome-wide association study of multiple sclerosis identifies KIF21B and TMEM39A as susceptibility loci. The genetic aspects of multiple sclerosis. The effect of single nucleotide polymorphisms from genome wide association studies in multiple sclerosis on gene expression. IL2RA gene polymorphism rs2104286 A>G seen in multiple sclerosis is associated with intermediate uveitis: possible parallel pathways?

Source and license

Adapted from rs12722489 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.