Proportionally a similar number of QTLs were observed for CpG methylation and mRNA expression. In order to determine whether SNP variability was more influential in CpG methylation or expression, we performed a random sampling, with 10,000 iterations, of QTL calculations for each independent measure in a core set of 100 individuals (Text S1). The results of this analysis show on average that 2.34% of CpG sites and 1.99% of mRNAs significantly correlate with QTLs. Each mRNA correlated with twice as many SNPs, on average, than CpG sites did. However the average R2 of the SNPs correlated with mRNAs was equal to CpGs (Figure S6).
