First, in terms of QTLs, we identified a set of eQTLs several times as large as those in previous studies, targeting a saturating proportion of protein-coding genes. Moreover, we were able to identify a substantial number of cQTLs. PsychENCODE was, in fact, among the first efforts to generate ChIP-seq data across a large cohort of brain samples, with experiments focused primarily on H3K27ac. In the future, further increasing cohort size and performing additional chromatin assays, such as STARR-seq (self-transcribing active regulatory region sequencing) and ChIP-seq for other histone modifications, will improve the identification of enhancers and cQTLs (52). More fundamentally, one-dimensional fluctuations in the chromatin signal reflect changes in three-dimensional chromatin architecture, and new metrics beyond cQTLs may be needed.
