We identified 1,050 (10.2%) hub SNPs that regulated the expression of >10 genes (Supplementary Table 6). Of these, 196 (18.6%) had a global up- or down-regulating effect on downstream genes (two-sided binomial test, Bonferroni-corrected P<0.05, Supplementary Table 6). We identified 507 (48%) hub SNPs showing enrichment for TF- or miRNA-binding sites (one-sided Fisher’s exact test, Benjamini-Hochberg FDR<0.05; Supplementary Table 7). For nine of these (5 independent loci), we observed that the respective TF was encoded by a gene positioned <1 Mb from the hub SNP, suggesting a TF-mediated mechanism. For example, rs1708733529 (dbSNP 137) affects the expression of 88 neuronal genes, possibly through the neuronal repressor encoded by nearby gene REST (Figure 4, Supplementary Note).
