Based on our results that reached statistical significance many QTLs appear to be tissue specific, where 49% of CpG sites and 54% of mRNA transcripts with a significant cis QTL were only detected within one tissue. Table 4 shows summary counts of CpG sites and mRNA transcripts with a QTL found in all four tissues. Because this analysis relies on a threshold for significance, it has the potential to be misleading, discounting QTLs that do not quite reach the threshold for significance. Thus, in order to compare detected methQTLs and eQTLs between tissues, we selected every SNP-CpG methylation pair and SNP-transcript pair that passed the defined threshold for significance in at least one tissue. We then compared R2 values for each of these SNP-CpG pairs or SNP-transcript pairs in all four tissues, including results from tissues where the SNP-CpG pair or SNP-transcript pair was non-significant, using ternary plots (Figure 4). The majority of large effect and many moderate effect QTLs were shared across the four brain regions (Figure 4) when significant effects from a tissue are compared with corresponding (possible
