The 888 reference brain transcriptomes were profiled from post-mortem brain samples of 783 individuals of European descent recruited by the ROS/MAP, Mayo, and Mount Sinai Brain Bank studies22,58,59. The transcriptomes were mainly profiled from the dPFC and also from frontal cortex, temporal cortex, inferior frontal gyrus, superior temporal gyrus, and perirhinal gyrus. Alignment, quality control, and normalization of RNA-sequencing data have been described in detail before30. Briefly, BAM files were converted to FASTQ format using Picard v.2.2.4, followed by alignment of reads to GRCh38 reference genome using STAR v.2.460. Gene-level counts were computed using STAR. Genes with < 1 count per million in at least 50% of the samples and with missing gene length and percent GC content were removed. Outlier samples were removed. Effects of batch, sex, post-mortem interval, age at death, final diagnosis of cognitive status, and brain region were regressed from these transcriptomes. Normalized gene expression values derived from alignment to GRCh38 were assigned the lift-over to GRCh37 gene coordinates for purposes of defining 1MB cis-variant windows used to acquire variants passing quality control and filtered for
