rs509749

A SNP in the LY9 gene on chromosome 1. Its most notable genotype is A;A: common; slight increase in SLE risk

Gene
LY9
Location
Chr 1160,823,770 (GRCh38)
Highest magnitude
0.0Typical
Tested on
23andMe, AncestryDNA, FamilyTreeDNA
Minor allele frequency
37%

Genotypes

As shown in 23andMe and AncestryDNA files.

  1. A;AMost notableNot ratedcommon; slight increase in SLE riskTypical · 0.011% of people
  2. A;GNot ratedcommon; slight increase in SLE riskTypical · 0.043% of people
  3. C;TNot ratedNo summary available.Typical · 0.00% of people
  4. G;GNot ratedrarer; slight decrease in SLE riskTypical · 0.046% of people

On SNPedia: (A;A), (A;G), (C;T), (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.

  • AverageA;A 11% A;G 43% C;T 0% G;G 46%
  • European ancestry (Utah)A;A 27% A;G 57% C;T 0% G;G 17%
  • Han Chinese (Beijing)A;A 10% A;G 37% C;T 0% G;G 54%
  • Japanese (Tokyo)A;A 5% A;G 39% C;T 0% G;G 56%
  • Yoruba (Nigeria)A;A 4% A;G 29% C;T 0% G;G 67%
  • African ancestry (Southwest US)A;A 9% A;G 51% C;T 0% G;G 40%
  • Chinese (Denver)A;A 5% A;G 43% C;T 0% G;G 52%
  • Gujarati IndianA;A 16% A;G 54% C;T 0% G;G 31%
  • Luhya (Kenya)A;A 4% A;G 26% C;T 0% G;G 71%
  • Mexican ancestry (Los Angeles)A;A 5% A;G 47% C;T 0% G;G 47%
  • Maasai (Kenya)A;A 12% A;G 39% C;T 0% G;G 49%
  • TuscanA;A 29% A;G 52% C;T 0% G;G 19%

Conditions, medicines and genes

Notes

From SNPedia

Notes

rs509749 is a SNP in exon 8 of the LY9 gene; this SNP is also known as Met602Val. The (A) allele encodes the Met; the (G) allele encodes the Val. The rarer (G) allele is undertransmitted in a family-based association study of systemic lupus erythematosus, leading to the conclusion that the (A) allele increases risk for SLE by increasing cytokine production and thereby enhancing the immune response.

Source and license

Adapted from rs509749 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 Its entries can be incomplete, out of date or wrong, and nothing here is a diagnosis or medical advice.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.