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 tests). Significant associations were reviewed in a mediation analysis with current versus never smoking as exposure, Dasen normalized beta-values of the CpG site as potential mediator and mRNA expression levels as outcome using the mediation package in R [33]. The method applied in the mediation package calculates the proportion of the association between tobacco smoking and expression that is mediated by methylation. This is done by comparing the effect estimates of tobacco smoking on expression in subjects with different levels of methylation.
