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Its strongest genetic-study result is p = 10−24, with 5 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 1,311,438 European ancestry individuals.
The effect
Each copy of the A allele shifted the measure 0.0147 higher (95% confidence interval 0.012-0.017); p = 6 × 10−25.
How common The A allele had a frequency of about 70% in the people studied.
Where it sits Chromosome 5, band 5q12.1 — in an intron of ZSWIM6.
How common each version is
AG
KoreanKRGDB
A 99.9% · G 0.1%
KoreanKorea1K
A 100.0% · G 0.1%
Japanese ToMMo
A 100.0% · G 0.0%
World gnomAD
A 69.9% · G 30.1%
World 1000 Genomes
A 76.7% · G 23.3%
World TOPMed
A 69.3% · G 30.7%
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.
What each result means
A/ATwo copies of the version the research linked to Educational attainment (MTAG). That is the strongest link of the three results. A link in a study is not a diagnosis.
A/GOne copy of the version the research linked to Educational attainment (MTAG). That is a smaller link than two copies.
G/GNo copy of the version the research linked to Educational attainment (MTAG). This is the starting point the study compared everyone against.
rs4490539 is a single position in the genome, in or near the ZSWIM6 gene. Published research associates it with educational attainment (mtag). A single variant does not decide an outcome — it shifts a probability, and for most common variants the shift is small.
What conditions is rs4490539 linked to?
On MyGeneLog this position is linked to Educational Attainment. The research behind each link, and its sources, are set out on that condition page.
Does having rs4490539 mean I will get this?
No. Common variants like this one move a probability slightly and, on their own, rarely decide anything about one person. Nothing on this page is a diagnosis, and health decisions should be made with a clinician who can see your whole picture.
Where does the information about rs4490539 come from?
GWAS Catalog, Nat Genet 2018, PMID:30038396. Every variant on MyGeneLog comes from public primary sources and is published with its citation and the date it was checked.
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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