Previous work has shown that SNPs are weakly correlated with the methylation status of CpG islands as compared to other DNA characteristics such as sequence and structure [15]; however we detected a large number of significant correlations detected between genetic variation and the methylation status of CpG sites (Table 2). Genome-wide visualization of detected methQTLs illustrated a strong positional effect of this relationship with an excess of the number and magnitude of cis associations (Figure 2A). The detected methQTLs accounted for between 18% and 88% of corrected methylation levels at individual loci. The number of CpG sites with methQTLs that were significant after correction for genome-wide multiple testing ranged from 1085 (4%) in the cerebellum to 1417 (5.1%) in the temporal cortex (Table 2). All significant methQTL results can be found in Table S3. Detection of cis QTL for DNA methylation was more likely when the CpG site was outside of an island (as defined in [14]); while 42% of sites on the array are within a CpG island, only 18% of the CpG sites with a significant QTL were in islands.
