there is an overlap of 1,042 variants associated with 315 DNA methylation probes and 183 transcript probes. A list of all variants associated with both DNA methylation and gene expression in cis is given in Supplementary Table 13. This overlapping set of variants likely includes multiple SNPs in LD that are associated with one gene expression transcript and DNA methylation site. Because the extent and magnitude of LD varies across the genome, we established an LD-independent set of SNPs associated with DNA methylation and tested the overlap of these with the sentinelized subsignals – i.e. the most associated marker from a set in high LD (r2 > 0.8) - from the brain eQTL dataset30. Compared to 1 million simulated mQTL SNP sets matched for allele frequency, this overlap was significantly greater than expected (relative enrichment = 4.23, P < 1.00×10−6 after 1 million simulations; Supplementary Table 14 and Supplementary Fig. 8).
