rs3819299

A SNP in the HLA-B gene on chromosome 6. Its most notable genotype is G;T: likely to carry one HLA-B27 allele, possible risk for B27 Syndromes.

Gene
HLA-B
Location
Chr 631,354,590 (GRCh38)
Highest magnitude
3.0Important
Tested on
23andMe, AncestryDNA, FamilyTreeDNA
Minor allele frequency
11%

Genotypes

Plus strand, as in 23andMe and AncestryDNA files.

  1. T;TGoodcommon in clinvarTypical · 0.089% of people
  2. G;TMost notableBadlikely to carry one HLA-B27 allele, possible risk for B27 Syndromes.Important · 3.011% of people
  3. G;GBadlikely to carry two HLA-B27 alleles, possible risk for B27 Syndromes.Important · 3.00% of people

SNPedia records rs3819299 on the minus strand: (A;A), (A;C), (C;C). 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 89% G;T 11% G;G 0%
  • European ancestry (Utah)T;T 92% G;T 8% G;G 0%
  • Han Chinese (Beijing)T;T 85% G;T 15% G;G 0%
  • Japanese (Tokyo)T;T 72% G;T 28% G;G 0%
  • Yoruba (Nigeria)T;T 99% G;T <1% G;G 0%
  • African ancestry (Southwest US)T;T 95% G;T 5% G;G 0%
  • Chinese (Denver)T;T 88% G;T 12% G;G 0%
  • Gujarati IndianT;T 82% G;T 18% G;G 0%
  • Luhya (Kenya)T;T 97% G;T 3% G;G 0%
  • Mexican ancestry (Los Angeles)T;T 85% G;T 16% G;G 0%
  • Maasai (Kenya)T;T 91% G;T 9% G;G 0%
  • TuscanT;T 97% G;T 3% G;G 0%

Other HLA-B SNPs

All HLA-B SNPs

Notes

From SNPedia

Show notes, about 150 words

Perhaps the best known HLA-B27 tag SNP is rs116488202, located about 23kb away from rs3819299, but the former SNP is not tested on many platforms (for example, it is not tested by Ancestry), while the latter is and can be used as a proxy assuming strong enough linkage disequilibrium (which is likely at least in European populations but perhaps not others). rs3819299 is reported to be associated with a (minor) impact on platelet count, but not with an association to ankylosing spondylitis (which is well reported as associated with HLA-B27). rs3819299 is cited in this patent as associated with HLA-B*4002 in the JPT population

G;T

See details at: HLA-B27 Syndromes. Not all allelles of HLA-B27 are at risk for B27 Syndromes, please check the HLA-B27 page for details.

G;G

See details at: HLA-B27 Syndromes. Not all allelles of HLA-B27 are at risk for B27 Syndromes, please check the HLA-B27 page for details.

Source and license

Adapted from rs3819299 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.