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Gut microbiota (bacterial taxa)

LINGO2 · rs10969143

Stands on its own. Nothing else here links to this position yet — but the page above is the point: what the research found, what each genotype means, and where it came from, in language you can read. Links to conditions, drugs and the senses appear automatically if we write them.

Strength of the evidence

1 / 4

Its strongest genetic-study result is p = 10−8, with 1 associations in the GWAS Catalog.

How this is scored

4: ClinVar disease-causing, reviewed by an expert panel or a guideline (3–4 stars). 3: ClinVar, several labs agreeing (2 stars), or a genetic study at p ≤ 10−50. 2: ClinVar from one lab (1 star), or p ≤ 10−20. 1: ClinVar submitted without criteria (0 stars), or genome-wide significance (p ≤ 5×10−8). The higher of the two counts. It says how solid the evidence is, not whether it matters for a particular person.

What the study found

Who was studied 984 European ancestry individuals; replicated in 530 European ancestry individuals.

The effect Each copy of the A allele shifted the measure 5.53 Z-score higher; p = 3 × 10−8.

Where it sits Chromosome 9, band 9p21.1 — between genes, 95.4 kb from PDK1P1.

How common each version is

AG
Korean KRGDB
A 49.1% · G 50.8%
Korean Korea4K
A 47.6% · G 52.4%
Japanese ToMMo
A 42.2% · G 57.8%
Vietnamese
A 47.2% · G 52.8%
World gnomAD
A 45.0% · G 55.0%
World 1000 Genomes
A 46.4% · G 53.6%
World TOPMed
A 45.1% · G 54.9%

By ancestry gnomAD

East Asian
A 46.9% · G 53.1%
European (non-Finnish)
A 46.0% · G 54.0%
African / African American
A 41.1% · G 58.9%
South Asian
A 43.8% · G 56.2%
Admixed American (Latino)
A 47.9% · G 52.1%
Middle Eastern
A 40.5% · G 59.5%
Finnish
A 50.7% · G 49.3%
Ashkenazi Jewish
A 43.0% · G 57.0%

The share of all copies of this position that are each version. Source: the population studies published in dbSNP (US NCBI); each row names its study. The ancestry rows are gnomAD's own groups (via Ensembl), as the survey defines them, not races.

What each result means

A/A Two copies of the version the research linked to Gut microbiota (bacterial taxa). That is the strongest link of the three results. A link in a study is not a diagnosis.
A/G One copy of the version the research linked to Gut microbiota (bacterial taxa). That is a smaller link than two copies.
G/G No copy of the version the research linked to Gut microbiota (bacterial taxa). This is the starting point the study compared everyone against.
Source
The effect of host genetics on the gut microbiome
Bonder MJ, Kurilshikov A, Tigchelaar EF, Mujagic Z, Imhann F, Vila AV, Deelen P, Vatanen T, Schirmer M, Smeekens SP, Zhernakova DV, Jankipersadsing SA
and 18 more — show all
Jaeger M, Oosting M, Cenit MC, Masclee AA, Swertz MA, Li Y, Kumar V, Joosten L, Harmsen H, Weersma RK, Franke L, Hofker MH, Xavier RJ, Jonkers D, Netea MG, Wijmenga C, Fu J, Zhernakova A
Nature genetics · 2016 · PMID 27694959

Quoting this page

Licensed CC BY-NC 4.0: free to read, share and adapt for non-commercial use, naming MyGeneLog™ and linking the exact page. Commercial use, including training or serving a commercial AI system, needs a licence — https://www.mygenelog.com/license

Gut microbiota (bacterial taxa) (rs10969143). MyGeneLog™. https://www.mygenelog.com/variants/rs10969143

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