Within each tissue, we selected every pairing of CpG methylation sites and mRNA transcripts where the CpG methylation site was within 1Mb of the mRNA TSS and both the CpG methylation site or mRNA transcript had a significant cis QTL. These CpG-mRNA pairs were then expanded into triplets of SNP and CpG-mRNA pair, where the SNP was significantly correlated in cis with either the CpG methylation site or mRNA transcript of the CpG-mRNA pair.
