rs3197999
A SNP in the MST1 gene on chromosome 3. Its most notable genotype is A;A: 1.2x risk of Crohn's
- Gene
- MST1
- Location
- Chr 349,684,099 (GRCh38)
- Highest magnitude
- 2.0Worth knowing
- Tested on
- 23andMe, AncestryDNA
- Minor allele frequency
- 22%
Genotypes
Plus strand, as in 23andMe and AncestryDNA files.
SNPedia records rs3197999 on the minus strand: (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.
- AverageA;A 4%
- European ancestry (Utah)A;A 5%
- Han Chinese (Beijing)A;A 0%
- Japanese (Tokyo)A;A 0%
- Yoruba (Nigeria)A;A 8%
- African ancestry (Southwest US)A;A 2%
- Chinese (Denver)A;A 2%
- Gujarati IndianA;A 4%
- Luhya (Kenya)A;A 9%
- Mexican ancestry (Los Angeles)A;A 2%
- Maasai (Kenya)A;A 8%
- TuscanA;A 8%
Related
Conditions, medicines and genes
Notes
From SNPedia
Show notes, about 150 words
via spitoon reports about which identifies 32 snps relevant to Crohn's disease: Out of a possible total of 46, 80% of people will have between 17 and 25 copies of the riskier versions of these SNPs. Because there are so many of these SNPs--and because the riskier versions are often more common than their less risky counterparts--even people at the high end of the distribution are not much more likely than average to develop Crohn's disease. *rs3197999 A 1.2 *rs2188962 T 1.25 *rs2476601 G 1.31 *rs2274910 C 1.14 *rs9286879 G 1.19 *rs10045431 C 1.11 *rs6908425 C 1.21 *rs2301436 T 1.21 *rs1456893 A 1.2 *rs1551398 A 1.08 *rs10758669 C 1.12 *rs3764147 G 1.25 *rs2872507 A 1.12 *rs744166 A 1.18 *rs762421 G 1.13 *rs3763313 C 1.19 Proxy snps on 23andMe *rs7714584 G 1.33 *rs6478108 T 1.22 *rs12122721 G 1.18 *rs7923172 A 1.16 *rs11564187 G 1.54 *rs1736148 T 1.18 *rs2024092 A 1.02
Source and license
Adapted from rs3197999 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 Its entries can be incomplete, out of date or wrong, and nothing here is a diagnosis or medical advice.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.