rs3095870

A SNP in the NKX2-5 gene on chromosome 5. Its most notable genotype is C;T: 1.7x increased risk for SLE (lupus)

Gene
NKX2-5
Location
Chr 5173,236,451 (GRCh38)
Highest magnitude
0.1Typical
Tested on
23andMe, AncestryDNA, FamilyTreeDNA
Minor allele frequency
23%

Genotypes

Plus strand, as in 23andMe and AncestryDNA files.

  1. T;TNot ratednormal riskTypical · 0.06% of people
  2. C;TMost notableBad1.7x increased risk for SLE (lupus)Typical · 0.132% of people
  3. C;CBad1.7x increased risk for SLE (lupus)Typical · 0.162% of people

SNPedia records rs3095870 on the minus strand: (A;A), (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.

  • AverageT;T 6% C;T 32% C;C 62%
  • European ancestry (Utah)T;T 13% C;T 46% C;C 41%
  • Han Chinese (Beijing)T;T 0% C;T 10% C;C 90%
  • Japanese (Tokyo)T;T <1% C;T 16% C;C 83%
  • Yoruba (Nigeria)T;T 6% C;T 29% C;C 65%
  • African ancestry (Southwest US)T;T 11% C;T 35% C;C 54%
  • Chinese (Denver)T;T 0% C;T 11% C;C 89%
  • Gujarati IndianT;T 20% C;T 40% C;C 41%
  • Luhya (Kenya)T;T <1% C;T 34% C;C 66%
  • Mexican ancestry (Los Angeles)T;T 3% C;T 53% C;C 43%
  • Maasai (Kenya)T;T 0% C;T 35% C;C 65%
  • TuscanT;T 12% C;T 46% C;C 42%

Conditions, medicines and genes

Other NKX2-5 SNPs

All NKX2-5 SNPs

Notes

From SNPedia

Notes

rs3095870 is a SNP in the promoter region of the NKX2.5 gene; it is also known as -1192C>T. rs3095870 has been linked to increased risk for systemic lupus erythematosus (SLE) in two independent Japanese case-control samples (p=0.0037 with odds ratio of 1.74, CI:1.19-2.55). Individuals with risk genotypes of both rs3748079 and rs3095870, in the ITPR3 and NKX2.5 genes, respectively, have even high risk for SLE (odds ratio 5.77, CI: 3.17-10.1). Note that the orientation of this SNP as published is reversed compared to the dbSNP entry.

Source and license

Adapted from rs3095870 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 Its entries can be incomplete, out of date or wrong, and nothing here is a diagnosis or medical advice.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.