To assess the enrichment of detected cis QTLs relative to those in trans we calculated the number of observed and possible cis and trans QTLs for CpG methylation and mRNA expression levels. The calculation of possible cis QTLs was performed by counting the number of all testable, genotyped SNPs within 1Mb of the CpG probe or transcript in question, regardless of significant association; calculation of possible trans QTLs was performed by counting the number of all testable, genotyped SNPs throughout the genome, excluding those within 1Mb of the CpG probe or transcript in question, again, regardless of significant association. This analysis was repeated for every tested CpG probe and transcript. These data showed an extreme enrichment of cis methylation and expression QTLs relative to trans (∼4400-fold and ∼7300-fold respectively). Although it should be noted that this calculation of enrichment does not take into account the differences in power to detect cis versus trans affects, thus the extreme nature of these fold changes may be inflated. While the average distance between correlated cis SNP and trait was 81Kb for CpG sites
