rs6498540

This is a downstream gene variant variant in the PDXDC1 gene.

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GWAS Catalog Trait Associations (30)

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

level of Phosphatidylcholine (18:0_20:3) in blood serum

Ottensmann L et al. “Genome-wide association analysis of plasma lipidome identifies 495 genetic associations.” Nature Communications 14(1):6934 (2023)
Allele G
OR 0.20
p 2.0e-29
N 7,169
Large GWAS
European
Tabassum R et al. “Lipidome- and Genome-Wide Study to Understand Sex Differences in Circulatory Lipids.” Journal of the American Heart Association 11(19):e027103 (2022)
Allele G
OR 0.20
p 1.0e-17
N 4,642
Large GWAS
European

level of Phosphatidylcholine (16:0_20:3) in blood serum

Ottensmann L et al. “Genome-wide association analysis of plasma lipidome identifies 495 genetic associations.” Nature Communications 14(1):6934 (2023)
Allele G
OR 0.19
p 2.0e-27
N 7,174
Large GWAS
European
Tabassum R et al. “Lipidome- and Genome-Wide Study to Understand Sex Differences in Circulatory Lipids.” Journal of the American Heart Association 11(19):e027103 (2022)
Allele G
OR 0.17
p 6.0e-9
N 2,624
Large GWAS
European

1-dihomo-linolenoyl-GPE (20:3n3 or 6) measurement

Surendran P et al. “Rare and common genetic determinants of metabolic individuality and their effects on human health.” Nature Medicine 28(11):2321-2332 (2022)
Allele A
OR 0.10
p 5.0e-19
N 14,296
Large GWAS
European

level of phosphatidylcholine

Lotta LA et al. “A cross-platform approach identifies genetic regulators of human metabolism and health.” Nature Genetics 53(1):54-64 (2021)
Allele A
OR 8.79
p 1.0e-18
N 16,837
Large GWAS
European
Harshfield EL et al. “Genome-wide analysis of blood lipid metabolites in over 5000 South Asians reveals biological insights at cardiometabolic disease loci.” Bmc Medicine 19(1):232 (2021)
Allele A
OR 0.08
p 1.0e-10
N 5,662
Large GWAS
South Asian

level of Phosphatidylcholine (18:1_20:3) in blood serum

Ottensmann L et al. “Genome-wide association analysis of plasma lipidome identifies 495 genetic associations.” Nature Communications 14(1):6934 (2023)
Allele G
OR 0.15
p 3.0e-18
N 7,171
Large GWAS
European
Tabassum R et al. “Lipidome- and Genome-Wide Study to Understand Sex Differences in Circulatory Lipids.” Journal of the American Heart Association 11(19):e027103 (2022)
Allele G
OR 0.15
p 5.0e-10
N 4,642
Large GWAS
European

free cholesterol to total lipids in chylomicrons and extremely 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 5.0e-18
N 450,015
Large GWAS
multi-ancestry

level of Phosphatidylcholine (O-16:0_20:3) in blood serum

Ottensmann L et al. “Genome-wide association analysis of plasma lipidome identifies 495 genetic associations.” Nature Communications 14(1):6934 (2023)
Allele G
OR 0.15
p 6.0e-17
N 6,709
Large GWAS
European

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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