rs10754339

A SNP in the VTCN1 gene on chromosome 1. Its most notable genotype is G;G: 1.45x increased risk of breast cancer

Gene
VTCN1
Location
Chr 1117,147,650 (GRCh38)
Highest magnitude
1.4Minor
Tested on
23andMe, AncestryDNA, FamilyTreeDNA
Minor allele frequency
24%

Genotypes

As shown in 23andMe and AncestryDNA files.

  1. A;AGoodnormalTypical · 0.057% of people
  2. A;GNot rated1.3x increased risk of breast cancerMinor · 1.326% of people
  3. G;GMost notableNot rated1.45x increased risk of breast cancerMinor · 1.418% of people

On SNPedia: (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.

  • AverageA;A 57% A;G 26% G;G 18%
  • European ancestry (Utah)A;A 85% A;G 14% G;G <1%
  • Han Chinese (Beijing)A;A 85% A;G 15% G;G 0%
  • Japanese (Tokyo)A;A 81% A;G 19% G;G <1%
  • Yoruba (Nigeria)A;A 8% A;G 33% G;G 59%
  • African ancestry (Southwest US)A;A 12% A;G 44% G;G 44%
  • Chinese (Denver)A;A 84% A;G 17% G;G 0%
  • Gujarati IndianA;A 76% A;G 24% G;G 0%
  • Luhya (Kenya)A;A 7% A;G 40% G;G 53%
  • Mexican ancestry (Los Angeles)A;A 81% A;G 17% G;G 2%
  • Maasai (Kenya)A;A 19% A;G 46% G;G 36%
  • TuscanA;A 84% A;G 15% G;G 1%

Conditions, medicines and genes

Other VTCN1 SNPs

All VTCN1 SNPs

Notes

From SNPedia

Notes

rs10754339 is a SNP in the V-set domain containing T cell activation inhibitor 1 VTCN1 gene, which is also known as B7-H4. A study of 500 Chinese Han women with breast cancer (and an equal number of matched controls) concluded that the rs10754339(A;G) genotype and G allele showed a significantly increased risk of breast cancer (odds ratio 1.455, CI: 1.119-1.892, and 1.325, CI: 1.073-1.637, respectively). Additionally, the rs10754339(G;G) genotype was significantly associated with lymph node metastasis and PR status, and the G allele and the (A;G) genotype were respectively associated with lymph node metastasis and ER status.

Source and license

Adapted from rs10754339 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 Its entries can be incomplete, out of date or wrong, and nothing here is a diagnosis or medical advice.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.