Of the 19 GWAS loci harboring SCZ-associated cis-eQTLs, eight involved only a single gene (i.e., no additional gene with relaxed adjusted Sherlock p < 0.5): furin (FURIN, down-regulated by risk allele), t-SNARE domain containing 1 (TSNARE1, up), contactin 4 (CNTN4, up), voltage-sensitive chloride channel 3 (CLCN3, up), synaptosomal-associated protein of 91 kDa (SNAP91, up), ENSG00000259946 (up), ENSG00000253553 (down), and the ENST00000528555 isoform of sorting nexin 19 (SNX19, down) (Fig. 2 and Supplementary Fig. 6B and 7A). For functional follow-up, we focused on the five single-gene loci encoding known proteins implicated at the gene level. First, we replicated these eQTL in the Religious Orders Study and Memory and Aging Project (ROS/MAP)26, with unpublished human DLPFC RNA sequencing data (N = 461). The most significant GWAS SNP was also a significant eQTL with the same direction of effect as in CMC for FURIN (rs4702: P = 1 × 10−6), CLCN3 (rs10520163: P = 9 × 10−6), and SNAP91 (rs3798869: P = 3 × 10−4); TSNARE1 (rs4129585: P = 0.057) and CNTN4 (rs17194490: P = 0.07) also had alleles in the same direction of effect as in CMC but did not reach significance.
