21). The number of eGenes, in fact, approaches the total number of genes estimated to be expressed in the brain. That said, a very large fraction of the smaller GTEx and CMC brain eQTL sets was contained within our set (as evident from overlap testing with the π1 statistic) (Fig. 4A) (36). Moreover, as expected, our brain eQTL set showed higher π1 similarity to and SNP-eGene overlap with GTEx brain eQTLs than with those from other tissues (Fig. 4B and fig. S31). Lastly, we applied the QTL pipeline to isoform levels to calculate a set of isoQTLs. We performed filtering in a variety of different ways, generating a number of different lists (21).
