Fig. 1

Schematic of possible meQTL effects. a Where the SNP and methylation site are within 1 Mb of each other, this is a “local” effect. All other effects are therefore “distant”, which is further sub-classified into same chromosome (b) and cross-chromosome (c) distant effects. As there are many millions of methylated sites in the genome, local SNPs with respect to one methylation site would be distant SNPs with respect to the vast majority of others. d The situation where a CpG-SNP affects methylation at a locus and thus causes a meQTL. Other SNPs in linkage disequilibrium (LD) with the CpG-SNP will also be associated with the CpG-SNP effect on methylation, and thus will appear to tag the meQTL