Genetic variants at hundreds of loci associated with cardiovascular phenotypes have been identified by genome wide association studies. Most of these variants are located in intronic or intergenic regions rendering the functional and mechanistic follow up difficult. These non-protein-coding regions harbor regulatory sequences. Thus the study of genetic variants associated with transcription—so called expression quantitative trait loci—has emerged as a promising approach to identify regulatory sequence variants. The genes and pathways they control constitute candidate causal drivers at cardiovascular risk loci. This review provides an overview of the expression quantitative trait loci resources available for cardiovascular genetics research and the most commonly used approaches for candidate gene identification.