For the 16,423 genes with above-threshold expression, gene-level eQTL (gene expression quantitative trait loci) were derived using the N = 467 genetically-inferred Caucasian samples (209 SCZ cases, 206 Controls, and 52 AFF cases), across the 6.4 million genotyped and imputed markers with imputation score (INFO) ≥ 0.8 and estimated minor allele frequency (MAF) ≥ 0.05. eQTL were computed using a linear model on the imputed genotype dosages using MatrixEQTL69. The gene expression data were adjusted for the covariate model, although without adjusting for ancestry vectors. In addition, the estimated Dx effect was added back to the residuals because we wanted to allow for an effect of diagnosis on gene expression. The 5 ancestry vectors were included instead in the eQTL model to control for ancestry differences in SNP allele frequencies. Thus, the final regression model for eQTL discovery in the full Caucasian CMC cohort was: adjusted gene expresion~SNP dosage+5 ancestry vectors+Dx FDR was estimated separately for cis-eQTL (defined as ≤ 1 MB between SNP marker and gene position) and trans-eQTL (> 1 MB between marker and gene), controlling for FDR
