Genetic associations with expression for genes implicated in GWAS studies for atherosclerotic cardiovascular disease and blood phenotypes

Hum Mol Genet. 2014 Feb 1;23(3):782-95. doi: 10.1093/hmg/ddt461. Epub 2013 Sep 20.


Genome-wide association studies (GWAS) have uncovered many genetic associations for cardiovascular disease (CVD). However, data are limited regarding causal genetic variants within implicated loci. We sought to identify regulatory variants (cis- and trans-eQTLs) affecting expression levels of 93 genes selected by their proximity to SNPs with significant associations in prior GWAS for CVD traits. Expression levels were measured by qRT-PCR in leukocytes from 1846 Framingham Heart Study participants. An additive genetic model was applied to 2.5 million imputed SNPs for each gene. Approximately 45% of genes (N = 38) harbored at least one cis-eSNP after a regional multiple-test adjustment. Applying a more rigorous significance threshold (P < 5 × 10(-8)), we found the expression level of 10 genes was significantly associated with more than one cis-eSNP. The top cis-eSNPs for 7 of these 10 genes exhibited moderate-to-strong association with ≥ 1 CVD clinical phenotypes. Several eSNPs or proxy SNPs (r(2) = 1) were replicated by other eQTL studies. After adjusting for the lead GWAS SNPs for the 10 genes, expression variances explained by top cis-eSNPs were attenuated markedly for LPL, FADS2 and C6orf184, suggesting a shared genetic basis for the GWAS and expression trait. A significant association between cis-eSNPs, gene expression and lipid levels was discovered for LPL and C6orf184. In conclusion, strong cis-acting variants are localized within nearly half of the GWAS loci studied, with particularly strong evidence for a regulatory role of the top GWAS SNP for expression of LPL, FADS2 and C6orf184.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Atherosclerosis / genetics*
  • Cardiovascular Diseases / genetics*
  • Computer Simulation
  • Fatty Acid Desaturases / genetics
  • Genetic Predisposition to Disease
  • Genome-Wide Association Study
  • Humans
  • Leukocytes / physiology
  • Lipids / blood
  • Lipids / genetics
  • Lipoprotein Lipase / genetics
  • Massachusetts
  • Models, Genetic
  • Polymorphism, Single Nucleotide*
  • Pseudogenes / genetics
  • Quantitative Trait Loci
  • Reproducibility of Results
  • Risk Factors


  • Lipids
  • Fatty Acid Desaturases
  • FADS2 protein, human
  • LPL protein, human
  • Lipoprotein Lipase