rs2651899

A SNP in the PRDM16 gene on chromosome 1. Its most notable genotype is C;C: 1.2x higher risk for migraines

Gene
PRDM16
Location
Chr 13,167,148 (GRCh38)
Highest magnitude
1.2Minor
Tested on
23andMe, AncestryDNA, FamilyTreeDNA
Minor allele frequency
50%

Genotypes

Plus strand, as in 23andMe and AncestryDNA files.

  1. C;TBad1.1x higher risk for migrainesMinor · 1.147% of people
  2. C;CMost notableBad1.2x higher risk for migrainesMinor · 1.229% of people

SNPedia records rs2651899 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 47% C;C 29%
  • European ancestry (Utah)C;T 44% C;C 20%
  • Han Chinese (Beijing)C;T 58% C;C 13%
  • Japanese (Tokyo)C;T 46% C;C 17%
  • Yoruba (Nigeria)C;T 42% C;C 52%
  • African ancestry (Southwest US)C;T 33% C;C 60%
  • Chinese (Denver)C;T 51% C;C 19%
  • Gujarati IndianC;T 44% C;C 28%
  • Luhya (Kenya)C;T 45% C;C 45%
  • Mexican ancestry (Los Angeles)C;T 52% C;C 19%
  • Maasai (Kenya)C;T 48% C;C 33%
  • TuscanC;T 59% C;C 18%

Conditions, medicines and genes

Notes

From SNPedia

Notes

rs2651899 is a SNP on ch 1p36.32 in the PRDM16 gene. A large GWAS study of over 5,000 patients with migraines and a meta-analysis concluded that this SNP was one of three influencing the condition, albeit with only slight risk increases on its own. The odds ratio for the slightly rarer rs2651899(G) allele was 1.11 (CI: 1.07 - 1.15, p = 3.8 x 10e-9). A 2013 study published by the American Headache Society reports significant influence of rs1835740, LRP1 rs11172113 and PRDM16 rs2651899 polymorphisms on migraine susceptibility in the Northern Indian population. Genome-wide-associated variants in migraine susceptibility: a replication study from North India.

Source and license

Adapted from rs2651899 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 Its entries can be incomplete, out of date or wrong, and nothing here is a diagnosis or medical advice.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.