These plots illustrate that the majority of eQTLs or methQTLs with strong effect sizes were consistent across tissues. For example, a large effect eQTL was found for CHURC1, which encodes a protein proposed to be involved in transcriptional regulation, in all tissues (Figure S7 and as reported previously [3]). However, there were also rare, but observable, events where a large effect QTL was detected within a single tissue and was completely absent in the other three tissues. For example the cis eQTL for PPAPDC1A, encoding a phosphatidic acid phosphatase that displays hydrolase and phosphotase activity at the membrane, has a large effect that appears to be restricted to the cerebellum, despite reliable detection of the transcript in all four brain regions (Figure 4Q and 4R–4T and Figure S8).
