Genetic variant

rs3197999

rs3197999 is a single-letter difference in human DNA, on chromosome 3. Carrying it does not, on its own, mean you have or will develop any condition.

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What is this?

Your DNA is a long sequence of four letters. At a few million positions, people commonly differ by a single letter; each of those positions is called a SNP (“snip”), and rs3197999 is the catalogue number of one of them. Which letters you carry there — one copy from each parent — is your genotype.

via spitoon reports about which identifies 32 snps relevant to Crohn's disease: '''Out of a possible...

From SNPedia

Why might it matter?

ClinVar holds no clinical classification for this variant. That is the usual case: most catalogued variants have no known effect on health.

Do I have this variant?

If you have taken a consumer DNA test (23andMe, AncestryDNA and similar), you can download its raw data file and check. Create a free account, upload the file, and this page will show the letters you carry at rs3197999, if your test read this position.

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Connect this with your blood results

A gene is a fixed instruction; a blood test shows what your body is doing now. CheckMyBloods reads the two side by side, so a variant can be set against the markers it could plausibly affect.

Blood markers do not diagnose a genetic condition, and a variant does not explain a blood result on its own. Together, with symptoms and family history, they give a clinician context.

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What should I do next?

  1. Find out whether you carry it. Reading about a variant says nothing about you until you know your genotype.
  2. Put it in context. Add your blood results, so the variant can be read against what your body is doing.
  3. Ask questions. Dr. Hemsworth, our AI assistant, can explain this variant and your results in plain English.
  4. Take anything that worries you to a professional. A GP or genetic counsellor can order a confirmatory test and interpret it with your history.
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This page is general information drawn from public research databases. It cannot diagnose anything, and it is not a substitute for advice from a doctor or genetic counsellor who knows your history.

Technical details

dbSNP ID
rs3197999
Position
chr3:49684099

Genome-wide association studies (20)

TraitRisk alleleOR / betaP-valueStudy
Hepatocyte growth factor-like protein levels A OR 1.2 2E-332 PubMed
Hepatocyte growth factor-like protein levels A OR 1.21 4E-303 PubMed
Serum levels of protein LHCGR A OR 0.62 1E-258 PubMed
Indoleamine 2,3-dioxygenase 1 levels A OR 0.38 1E-155 PubMed
Leukocyte cell-derived chemotaxin 1 levels A OR 0.35 3E-131 PubMed
G3XAK1 protein level (protein group normalized intensity) A OR 0.78 2E-119 PubMed
Transmembrane protease serine 11D levels (TMPRSS11D.6547.83.3) A OR 0.53 3E-96 PubMed
Interleukin-23 receptor levels A OR 0.28 5E-90 PubMed
Serum levels of protein TMPRSS11D A OR 0.31 2E-61 PubMed
Chronic inflammatory diseases (ankylosing spondylitis, Crohn's disease, psoriasis, primary sclerosing cholangitis, ulcerative colitis) (pleiotropy) — — 7E-55 PubMed
Tensin-2 levels A OR 0.22 8E-49 PubMed
Tensin-2 levels (TNS2.11667.29.3) A OR 0.38 4E-48 PubMed
Inflammatory bowel disease A OR 1.18 1E-47 PubMed
Regenerating islet-derived protein 3-alpha protein levels (SomaScan ID:4407-10) A OR 1.2 3E-46 PubMed
Ulcerative colitis A OR 1.19 2E-37 PubMed
Inflammatory bowel disease — — 1E-33 PubMed
Crohn's disease A OR 1.17 2E-33 PubMed
Erythrocyte band 7 integral membrane protein levels A OR 0.17 4E-31 PubMed
Dedicator of cytokinesis protein 9 levels (DOCK9.14002.18.3) A OR 0.3 1E-28 PubMed
Primary sclerosing cholangitis A OR 1.33 2E-26 PubMed

Sources