At the tissue level, we used data from 53 human tissues (Genotype-Tissue Expression (GTEx) project version 7)8; at the cell type level, we used mouse data from 5 different brain regions broadly-defined (24 cell types) and narrowly-defined (149 cell types)9. Analyses were performed using MAGMA and partitioned LD score regression as previously described9 with minor modifications. Briefly, for the single cell data set9, gene expression for each cell type was scaled to 1,000,000 unique molecular identifiers (UMI) prior to computing specificity scores (defined as the proportion of total expression of specific genes performed in a given cell type). Median transcripts per million (TPM) across individuals were downloaded from the GTEx portal website (https://gtexportal.org/) and used to compute specificity scores. For each tissue or cell-type, the specificity scores were then rank-transformed to a standard normal distribution usingthe rntranform function from the GenABEL R package46. Using MAGMA, the standard normalized specificity scores were then regressed on gene-wise association, defined as the mean p-value across all SNPs assigned to the gene (+35kb upstream to −10kb downstream). Using partitioned LD score regression47, we selected
