Since DNA methylation may have an effect on gene expression, we tested the association between DNA methylation and mRNA expression of nearby CAD-related genes. In the 724 individuals under study, 16 genes out of 26 candidates were found to be expressed in blood. First, we regressed out the Houseman-estimated white blood cell proportions, the erythrocytes and platelet cell counts, fasting state, RNA quality score, plate number, age and sex on the mRNA expression levels using a linear mixed model. We then regressed out the Houseman-estimated white blood cell proportions, age, sex, array number and position on array on the Dasen normalized beta-values of the CpG sites using a linear mixed model. The residuals of the mRNA expression levels and the residuals of the Dasen normalized beta-values of the CpG sites were checked for association using a linear regression model. We analysed the associations between the 15 methylation sites and 16 nearby CAD genes. Additional file 1: Table S3 indicates the 35 CpG-gene combinations that were tested. The robust Bonferroni-corrected p-value threshold for a significant association was 1.4 × 10−3 (0.05/35
