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 the top 10% most specific genes for each tissue/cell type, extended the coordinates of each gene by 100kb upstream and downstream, and tested for heritability enrichment of these regions48. Results from both methods were integrated by averaging the -log10 p-values obtained for each tissue/cell type. Bonferroni multiple-testing correction was applied for all tests performed in this analysis (0.05/(53+24+149)).
