In addition to the replication design described above, we also performed functional eQTL analysis on the replicable risk SNPs, which included (1) cis-eQTL analysis on exon-/transcript-level expression changes in peripheral blood mononucleated cells (PBMCs) (n=80) and cortical brain tissues (n=93), (2) transcriptome-wide trans-acting eQTL analysis on transcript expression, (3) genome-wide trans-acting eQTL analysis on the transcript expression of the replicable risk genes, and (4) transcriptome-wide expression correlation analysis [Heinzen et al., 2008; Zuo et al., 2011a; Zuo et al., 2011b]. Additionally, RNA secondary structure analysis [Zuker 2003; Zuo et al., 2011a; Zuo et al., 2011b] and a series of bioinformatic analysis (Supplemental Table S2) of the replicable risk markers were also performed.
