We used partitioned LD score regression 95 to test whether the top 10% most specific genes of each cell type (based on our specificity metric described above) were enriched in heritability for the diverse traits. Only genes with at least 1TPM or 1 UMI per million in the tested cell type were used for this analysis. In order to capture most regulatory elements that could contribute to the effect of the region on the trait, we extended the gene coordinates by 100kb upstream and by 100kb downstream of each gene as previously 13. SNPs located in 100kb regions surrounding the top 10% most specific genes in each cell type were added to the baseline model (consisting of 53 different annotations) independently for each cell type (one file for each cell type). We then selected the coefficient z-score p-value as a measure of the association of the cell type with the traits. The significance threshold was set to a 5% false discovery rate across all tissues/cell types and traits within each dataset. All plots show the mean −log10(P) of partitioned LDscore regression and MAGMA. All results for MAGMA or LDSC are available in supplementary data files.
