For this 4.8% with a shared QTL both the mean distance between the CpG site and mRNA TSS and the strength of the correlation differed from that of the considered combinations. For the shared QTLs the distance between CpG site and mRNA TSS is 27.5Kb whereas in all considered the mean distance was 394.4Kb. The mean R2 between CpG methylation and mRNA expression within the shared QTL set was 0.255 as compared to 0.033 in the considered set. Within these possibly shared QTLs, almost half of the significant methQTLs and eQTLs were correlated in the same direction, i.e. the CpG methylation level was positively correlated with the mRNA expression level (Figure S9). However; when considering only those shared QTLs where the CpG site was within a CpG island (as defined in [14]), 91% of these CpG methylation sites and mRNA expression pairs are inversely correlated, in line with the traditional view that increased CpG island methylation is associated with decreased expression at geographically local transcripts (Figure 5).
