Six risk variants for colon polyps, surfaced from a 220-phenotype genetic atlas built across Japanese, European, and Finnish populations — one small slice of a much bigger study.
Colon polyps are growths on the lining of the colon, some of which can become cancerous over time. This page covers six variants tied to colon polyp risk, drawn from a much larger genetic study that examined 220 different health traits at once.
A 2021 study in Nature Genetics built a phenome-wide genetic atlas using BioBank Japan (179,000 people), incorporating past medical history and text-mining of electronic medical records, then meta-analyzed it with the UK Biobank and FinnGen (a combined 628,000 people). Across all 220 phenotypes studied — diseases, biomarkers, and medication usage — the atlas found roughly 5,000 new genetic loci in total.
Colon polyp is one of those 220 phenotypes. Six of the associations this catalogue links to it come from that atlas: rs79231157 (BOC), rs9475429 (BMP5), rs7100296 (VTI1A), rs117629395 (SIRT3), rs422249 (near FADS3), and rs11169562 (ATF1). The study's own abstract does not report a colon-polyp-specific locus count, gene list, or effect size beyond what is captured in these six associations.
The study's own headline findings are about the atlas as a whole, not about colon polyps: mapping the landscape of pleiotropy at the major histocompatibility complex (MHC) locus through HLA fine-mapping, and a statistical decomposition of the full phenome-wide results into latent genetic components that helped identify subtypes of related diseases (the paper's own example is allergic disease). None of that is specific to colon polyps, and none of it is claimed here.
Positions joined since this page was written
What this is The text above discusses the variants this page was written around. Since then the catalogue has joined 1 more position to it, by shared trait or shared paper. They are listed here by the paper each came from; the text does not describe them, and each variant page carries that study's own record.
Verma A et al. 2024, Science (New York, N.Y.) rs535025308 (CHRDL2) — PMID:39024449
Colon polyps are found and removed through colonoscopy, not diagnosed by genotype. These six variants are associations from a broad, 220-phenotype genetic atlas, not a screening tool or a substitute for colonoscopy at the recommended age.
Because colon polyp was one of 220 phenotypes examined in this study rather than its focus, the depth of evidence behind any single one of these six loci is necessarily lighter than a study built specifically around colon polyps would provide.
What a 23andMe/AncestryDNA export or raw VCF can and can't tell you about Colon Polyp comes down to these specific, well-studied positions — not a diagnosis.
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Colon Polyp. MyGeneLog™. https://www.mygenelog.com/conditions/colon-polyp
A colon polyp is a growth on the lining of the colon. Some types can become cancerous over time, which is why colonoscopy screening looks for and removes them.
No. The six variants here come from a 2021 genetic atlas that examined 220 different health phenotypes at once across Japanese, UK, and Finnish populations — colon polyp was one of the 220, not the study’s own focus.
No. Colon polyps are found through colonoscopy. These variants are research associations, not a validated screening or diagnostic tool.
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