The 150 SNPs identified in the CAD GWAS were annotated to 85 genes with an in-gene variant and 84 cis-expression-quantitative trait loci (cis-eQTL) within 1 Mb of the identified SNPs as found in a large publically available blood cis-eQTL database (FDR < 0.05) (Additional file 1: Table S1) [9]. These genes had 3669 methylation sites measured on the array within and near the gene as provided by Illumina (Additional file 1: Table S2). After correction for multiple testing, 15 CpG sites were significantly associated with current smoking (p < 1.4 × 10−5) (Table 2). Current tobacco smoking was associated with a 1.2 to 2.4 % lower DNA methylation compared to never smoking in 12 of the CpG sites. In three CpG sites, current tobacco smoking was associated with a 1.2 to 1.8 % higher DNA methylation. The effect estimates of the associations were robust to further adjustment for total cholesterol, triglyceride levels, systolic blood pressure, daily alcohol intake and type 2 diabetes mellitus as potential confounders or mediators. In a sensitivity analysis in current smokers, two sites were significantly associated
