rs1169289

This variant is located in the HNF1A gene.

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GWAS Catalog Trait Associations (24)

Genome-wide significant associations (p < 5×10⁻⁸) from the NHGRI-EBI GWAS Catalog.

cholesterol to total lipids in large VLDL percentage

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele G
OR 0.02
p 2.0e-29
N 450,015
Large GWAS
multi-ancestry

cholesteryl esters to total lipids in large VLDL percentage

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele G
OR 0.02
p 9.0e-28
N 450,015
Large GWAS
multi-ancestry

cholesteryl esters to total lipids in small VLDL percentage

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele G
OR 0.02
p 2.0e-24
N 450,015
Large GWAS
multi-ancestry

triglycerides to total lipids in medium VLDL percentage

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele G
OR 0.02
p 1.0e-22
N 450,015
Large GWAS
multi-ancestry

free cholesterol to total lipids in large VLDL percentage

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele G
OR 0.02
p 1.0e-19
N 450,015
Large GWAS
multi-ancestry

cholesterol to total lipids in small VLDL percentage

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele G
OR 0.02
p 4.0e-19
N 450,015
Large GWAS
multi-ancestry

cholesterol to total lipids in medium VLDL percentage

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele G
OR 0.02
p 8.0e-19
N 450,015
Large GWAS
multi-ancestry

reticulocyte count

Loya H et al. “A scalable variational inference approach for increased mixed-model association power.” Nature Genetics 57(2):461-468 (2025)
Allele G
OR 0.02
p 2.0e-17
N 394,642
Large GWAS
European

cholesteryl esters to total lipids in medium VLDL percentage

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele G
OR 0.02
p 3.0e-16
N 450,015
Large GWAS
multi-ancestry

reticulocyte amount

Loya H et al. “A scalable variational inference approach for increased mixed-model association power.” Nature Genetics 57(2):461-468 (2025)
Allele G
OR 0.02
p 3.0e-16
N 394,642
Large GWAS
European
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ClinVar annotation

Conflicting Classifications
10 submitters22 publications

not specified; Maturity-onset diabetes of the young type 3; not provided; Type 2 diabetes mellitus; Maturity-onset diabetes of the young; Nonpapillary renal cell carcinoma

View on ClinVar →

About HNF1A

The protein encoded by this gene is a transcription factor required for the expression of several liver-specific genes. The encoded protein functions as a homodimer and binds to the inverted palindrome 5'-GTTAATNATTAAC-3'. Defects in this gene are a cause of maturity onset diabetes of the young type 3 (MODY3) and also can result in the appearance of hepatic adenomas. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Apr 2015]

View all HNF1A variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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