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Hypothyroidism

PTPN1 · rs6512654

Where this position leads

Condition: Hypothyroidism

rs6512654 Condition: Hypothyroidism Hypothyroidism Condition rs6512654 rs6512654 PTPN1

What the study found

Who was studied 221,596 European ancestry cases, 1,564,466 European ancestry controls.

The effect Each copy of the G allele shifted the measure 0.0337 higher (95% confidence interval 0.022-0.045); p = 8 × 10−9.

How common The G allele had a frequency of about 11% in the people studied.

Where it sits Chromosome 20, band 20q13.13 — in an intron of PTPN1.

What each result means

G/G Published research associates this genotype (two copies of the reported risk allele) with a higher likelihood of Hypothyroidism compared to the general population.
G/T Published research associates this genotype (one copy of the reported risk allele) with an intermediate association with Hypothyroidism.
T/T Published research associates this genotype with typical/baseline likelihood of Hypothyroidism — no copies of the reported risk allele.
Source
Global multi-ancestry genome-wide analyses identify genes and biological pathways associated with thyroid cancer and benign thyroid diseases
White SL, Brasher MS, Pattee J, Zhou W, Chapman S, Jee YH, Bell CC, Jamil TL, Barrio M, Arehart CH, Evans LM, Hirbo J
and 73 more — show all
Cox NJ, Straub P, Namba S, Bertucci-Richter E, Guare L, Edris A, Morris S, Mulford AJ, Zhang H, Fennessy B, Tobin MD, Chen J, Williams AT, John C, van Heel DA, Mathur R, Finer S, Moksnes MR, Brumpton BM, Åsvold BO, Peculis R, Rovite V, Konrade I, Wang Y, Crooks K, Chavan S, Fisher MJ, Rafaels N, Lin M, Shortt JA, Sanders AR, Whiteman DC, MacGregor S, Medland SE, Thorsteinsdóttir U, Stefánsson K, Karaderi T, Egan KM, Bocklage T, McCrary HC, Riedlinger G, Salhia B, Shriver C, Phan MD, Farlow JL, Edge S, Kaur V, Churchman ML, Rounbehler RJ, Brock PL, Ringel MD, Pividori M, Schweppe R, Raeburn CD, Walters RG, Chen Z, Li L, Matsuda K, Okada Y, Zöllner S, Verma A, Preuss MH, Kenny E, Hendricks AE, Fishbein L, Kraft P, Daly MJ, Neale BM, Martin AR, Cole JB, Haugen BR, Gignoux CR, Pozdeyev N
Penn Medicine BioBank · Virtual Thyroid Biopsy Consortium · Colorado Center for Personalized Medicine · Genes & Health Research Team · BioBank Japan Project · Global Biobank Meta-analysis Initiative
Nature genetics · 2026 · PMID 41644669 · open access

Questions about rs6512654

What is rs6512654?

rs6512654 is a single position in the genome, in or near the PTPN1 gene. Published research associates it with hypothyroidism. A single variant does not decide an outcome — it shifts a probability, and for most common variants the shift is small.

What conditions is rs6512654 linked to?

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

Does having rs6512654 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 rs6512654 come from?

GWAS Catalog, Nature genetics 2026, PMID:41644669. 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.

Hypothyroidism (rs6512654). MyGeneLog™. https://www.mygenelog.com/variants/rs6512654

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