To screen for cis-acting genetic regulation of splicing/expression genetic association analyses were conducted to search for cis-acting SNPs that regulate exon-level and gene-level expression. Specifically, associations were limited to SNPs lying in or 100 kb surrounding the region of the transcripts or exons. Linear regression incorporating all the covariates was performed using PLINK genome-wide association analysis toolkit (http://pngu.mgh.harvard.edu/∼purcell/plink/) [26]. To control for the possibility of spurious associations resulting from population stratification, we used a modified EIGENSTRAT method [13,27]. A total of four separate analyses were conducted, including PBMC transcript level, PBMC exon level, brain transcript level, and brain exon level. Thresholds for significance at each level were calculated based on the total number of association tests conducted within the four separate analyses.
