rs3129934

A SNP in the LOC101929163 gene on chromosome 6. Its most notable genotype is T;T: 3.3x increased risk for multiple sclerosis

Gene
LOC101929163
Location
Chr 632,368,410 (GRCh38)
Highest magnitude
2.2Worth knowing
Tested on
23andMe, AncestryDNA
Minor allele frequency
14%

Genotypes

As shown in 23andMe and AncestryDNA files.

  1. C;CGoodNormal lower risk of Multiple Sclerosis.Worth knowing · 2.174% of people
  2. C;TBadIncreased risk of Multiple Sclerosis.Worth knowing · 2.024% of people
  3. T;TMost notableBad3.3x increased risk for multiple sclerosisWorth knowing · 2.23% of people

On SNPedia: (C;C), (C;T), (T;T). 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;C 74% C;T 24% T;T 3%
  • European ancestry (Utah)C;C 66% C;T 29% T;T 5%
  • Han Chinese (Beijing)C;C 88% C;T 10% T;T 2%
  • Japanese (Tokyo)C;C 99% C;T <1% T;T 0%
  • Yoruba (Nigeria)C;C 56% C;T 38% T;T 6%
  • African ancestry (Southwest US)C;C 68% C;T 28% T;T 4%
  • Chinese (Denver)C;C 76% C;T 22% T;T 2%
  • Gujarati IndianC;C 89% C;T 10% T;T 1%
  • Luhya (Kenya)C;C 61% C;T 38% T;T <1%
  • Mexican ancestry (Los Angeles)C;C 74% C;T 22% T;T 3%
  • Maasai (Kenya)C;C 56% C;T 38% T;T 6%
  • TuscanC;C 78% C;T 23% T;T 0%

Conditions, medicines and genes

Other LOC101929163 SNPs

All LOC101929163 SNPs

Notes

From SNPedia

Show notes, about 210 words

rs3129934 is a SNP near the HLA-class II region that may be associated with several autoimmune diseases. In a study of two cohorts (Spanish and American multiple sclerosis patients, each numbering several hundred), rs3129934 was the SNP most associated with increased risk for multiple sclerosis. The odds ratio was 3.3 (CI: 2.3 - 4.9, p = 9 x 10e-11). Seven other SNPs were also identified in this study as associated with increased risk for MS. associated with type-1 diabetes. 1.6x risk of type-1 diabetes? 23andMe uses rs9273363 instead of rs3129934 in its reports on type 1 diabetes risk. This SNP was formerly used as a proxy for rs9272346, with this explanation: "Note: the 2007 Wellcome Trust paper reported a strong association between type 1 diabetes and the SNP rs9272346. Our quality control process flagged data for rs9272346 as unreliable, so we instead included the SNP rs3129934, which is also highly associated with type 1 diabetes. Both are in the HLA region, although the exact linkage patterns between tagging SNPs and traditionally determined HLA haplotypes is still being worked out." However it is apparent that the HapMap frequencies for these two snps are very different. rs9291683, rs3129934 and rs2705293 discussed in the context of CNVs in a blog post

Source and license

Adapted from rs3129934 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.