rs12928099
This is a regulatory region variant variant in the PDXDC1 gene.
▶GWAS Catalog Trait Associations (88)
Genome-wide significant associations (p < 5×10⁻⁸) from the NHGRI-EBI GWAS Catalog.
GWAS Catalog Trait Associations (88)
Genome-wide significant associations (p < 5×10⁻⁸) from the NHGRI-EBI GWAS Catalog.
saturated fatty acids to total fatty acids percentage
Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele A
OR 0.07
p 2.0e-258
N 450,015
Large GWAS
multi-ancestry
degree of unsaturation measurement
Davyson E et al. “Metabolomic Investigation of Major Depressive Disorder Identifies a Potentially Causal Association With Polyunsaturated Fatty Acids.” Biological Psychiatry 94(8):630-639 (2023)
Allele A
OR 0.10
p 1.0e-84
N 88,268
Large GWAS
European
VLDL particle size
Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele A
OR 0.04
p 2.0e-67
N 450,015
Large GWAS
multi-ancestry
phospholipids in chylomicrons and extremely large VLDL measurement
Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele A
OR 0.03
p 9.0e-56
N 450,015
Large GWAS
multi-ancestry
triglycerides to phosphoglycerides ratio
Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele A
OR 0.03
p 2.0e-53
N 450,015
Large GWAS
multi-ancestry
triglycerides to total lipids in very large HDL percentage
Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele A
OR 0.03
p 7.0e-53
N 450,015
Large GWAS
multi-ancestry
free cholesterol in chylomicrons and extremely large VLDL measurement
Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele A
OR 0.03
p 1.0e-52
N 450,015
Large GWAS
multi-ancestry
cholesterol in chylomicrons and extremely large VLDL measurement
Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele A
OR 0.03
p 2.0e-52
N 450,015
Large GWAS
multi-ancestry
total lipids in chylomicrons and extremely large VLDL measurement
Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele A
OR 0.03
p 1.0e-51
N 450,015
Large GWAS
multi-ancestry
docosahexaenoic acid measurement, fatty acid amount
Karjalainen MK et al. “Genome-wide characterization of circulating metabolic biomarkers.” Nature 628(8006):130-138 (2024)
Allele A
OR 0.07
p 6.0e-51
N 136,016
Large GWAS
multi-ancestry
About PDXDC1
Enables cadherin binding activity. Predicted to be involved in carboxylic acid metabolic process. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Jul 2025]
View all PDXDC1 variants →Gene information from NCBI Gene. Variant classifications from ClinVar.
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