Gene Knowledge Graph
UTC

Links from this page to related variants, conditions, drugs and topics are not included for automated readers. Those connections are the Gene Knowledge Graph and are licensed as data: https://www.mygenelog.com/license

Standard

HDL cholesterol

near CYCSP42 · rs9978541

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 315,133 European ancestry individuals, 74,970 East Asian ancestry individuals.

The effect Each copy of the G allele shifted the measure 0.0144 lower (95% confidence interval 0.0097-0.0191); p = 4 × 10−9.

Where it sits Chromosome 21, band 21q21.1 — between genes, 9 kb from CYCSP42.

How common each version is

GT
Korean KRGDB
G 21.9% · T 78.1%
Korean Korea4K
G 21.0% · T 79.0%
Korean Korea1K
G 21.2% · T 78.8%
Vietnamese
G 30.1% · T 69.9%
World gnomAD
G 37.3% · T 62.7%
World 1000 Genomes
G 41.6% · T 58.4%
World TOPMed
G 39.2% · T 60.8%

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

G/G Two copies of the version the research linked to HDL cholesterol. That is the strongest link of the three results. A link in a study is not a diagnosis.
G/T One copy of the version the research linked to HDL cholesterol. That is a smaller link than two copies.
T/T No copy of the version the research linked to HDL cholesterol. This is the starting point the study compared everyone against.
Source
A cross-population atlas of genetic associations for 220 human phenotypes
Sakaue S, Kanai M, Tanigawa Y, Karjalainen J, Kurki M, Koshiba S, Narita A, Konuma T, Yamamoto K, Akiyama M, Ishigaki K, Suzuki A
and 34 more — show all
Suzuki K, Obara W, Yamaji K, Takahashi K, Asai S, Takahashi Y, Suzuki T, Shinozaki N, Yamaguchi H, Minami S, Murayama S, Yoshimori K, Nagayama S, Obata D, Higashiyama M, Masumoto A, Koretsune Y, Ito K, Terao C, Yamauchi T, Komuro I, Kadowaki T, Tamiya G, Yamamoto M, Nakamura Y, Kubo M, Murakami Y, Yamamoto K, Kamatani Y, Palotie A, Rivas MA, Daly MJ, Matsuda K, Okada Y
FinnGen
Nature genetics · 2021 · PMID 34594039

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

HDL cholesterol (rs9978541). MyGeneLog™. https://www.mygenelog.com/variants/rs9978541

← See all variants