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Seborrheic keratosis (PheCode 702.2)

near PKP1 · rs1539690

Where this position leads

Condition: Seborrheic Keratosis

rs1539690 Condition: Seborrheic Keratosis Seborrheic Keratosis Condition rs1539690 rs1539690 near PKP1

What the study found

Who was studied 3,192 African American or Afro-Caribbean cases, 112,982 African American or Afro-Caribbean controls, 4,518 Hispanic or Latin American cases, 50,328 Hispanic or Latin American controls, 356 East Asian ancestry cases, 6,050 East Asian ancestry controls, 88,990 European ancestry cases, 303,479 European ancestry controls.

The effect Each copy of the G allele shifted the measure 0.0482 higher (95% confidence interval 0.035-0.061); p = 8 × 10−14.

How common The G allele had a frequency of about 53% in the people studied.

Where it sits Chromosome 1, band 1q32.1 — between genes, 3.1 kb from PKP1.

What each result means

A/A No copy of the version the research linked to Seborrheic keratosis (PheCode 702.2). This is the starting point the study compared everyone against.
A/G One copy of the version the research linked to Seborrheic keratosis (PheCode 702.2). That is a smaller link than two copies.
G/G Two copies of the version the research linked to Seborrheic keratosis (PheCode 702.2). That is the strongest link of the three results. A link in a study is not a diagnosis.
Source
Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program
Verma A, Huffman JE, Rodriguez A, Conery M, Liu M, Ho YL, Kim Y, Heise DA, Guare L, Panickan VA, Garcon H, Linares F
and 59 more — show all
Costa L, Goethert I, Tipton R, Honerlaw J, Davies L, Whitbourne S, Cohen J, Posner DC, Sangar R, Murray M, Wang X, Dochtermann DR, Devineni P, Shi Y, Nandi TN, Assimes TL, Brunette CA, Carroll RJ, Clifford R, Duvall S, Gelernter J, Hung A, Iyengar SK, Joseph J, Kember R, Kranzler H, Kripke CM, Levey D, Luoh SW, Merritt VC, Overstreet C, Deak JD, Grant SFA, Polimanti R, Roussos P, Shakt G, Sun YV, Tsao N, Venkatesh S, Voloudakis G, Justice A, Begoli E, Ramoni R, Tourassi G, Pyarajan S, Tsao P, O'Donnell CJ, Muralidhar S, Moser J, Casas JP, Bick AG, Zhou W, Cai T, Voight BF, Cho K, Gaziano JM, Madduri RK, Damrauer S, Liao KP
Science (New York, N.Y.) · 2024 · PMID 39024449 · open access

Questions about rs1539690

What is rs1539690?

rs1539690 is a single position in the genome, in or near the near PKP1 gene. Published research associates it with seborrheic keratosis (phecode 702.2). A single variant does not decide an outcome — it shifts a probability, and for most common variants the shift is small.

What conditions is rs1539690 linked to?

On MyGeneLog this position is linked to Seborrheic Keratosis. The research behind each link, and its sources, are set out on that condition page.

Does having rs1539690 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 rs1539690 come from?

GWAS Catalog, Science (New York, N.Y.) 2024, PMID:39024449. Every variant on MyGeneLog comes from public primary sources and is published with its citation and the date it was checked.

Quoting this page

Free to quote and reuse under CC BY 4.0. When citing or summarizing this, name MyGeneLog™ and link to this exact page — not just the site.

Seborrheic keratosis (PheCode 702.2) (rs1539690). MyGeneLog™. https://www.mygenelog.com/variants/rs1539690

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