Of the 150 SNPs discovered by CARDIoGRAMplusC4D, 96 were located within a gene [1]. In addition, 58 SNPs had known effect on expression of a gene within 1 Mb as found in a large publically available blood cis-eQTL database (FDR < 0.05) [9]. We annotated these SNPs to 85 genes with an in-gene variant and 84 cis-eQTL genes (Additional file 1: Table S1). The methylation probes within and near these CAD-related genes as provided by Illumina were included in the analysis. We excluded probes from the Infinium HD methylation SNP list with a minor allele frequency above 1 % as provided by Illumina, since variations in these SNPs can cause bias in the methylation measurement [25]. We further excluded known cross-reactive probes, since they can introduce bias in the results [26]. A complete list of the probes considered for analysis including reasons for exclusion can be found in Additional file 1: Table S2. The remaining 3669 methylation probes were checked for association with tobacco smoking using a linear mixed model with the LME4 package in R version 3.1.0 with Dasen
