Expression quantitative trait loci (eQTL) data from lymphoblast cell lines (LCLs), cerebellum, and frontal cortex were generated as described previously.26-27 Similarly, methylation QTLs (mQTLs), which represent SNPs that are associated with variation in genome-wide patterns of methylation, were derived from adult cerebellum.28 The top distribution of GWAS SNPs from the primary meta-analysis, 412 LD-pruned SNPs with p<0.001, were tested for eQTL or mQTL enrichment compared to 1000 randomly-drawn, LD-pruned sets of allele-frequency matched SNPs taken from the set of typed SNPs on the Illumina 550K (Supplementary Methods). The number of eQTLs (or mQTLs) in each simulated set yielded an empirical distribution and enrichment p-value, calculated as the proportion of randomized sets in which the eQTL/mQTL count matched or exceeded the actual observed count in the list of top SNP associations. A similar analysis was performed to test for enrichment of missense SNPs or SNPs within a gene as defined by dbSNP annotation.
