In addition to stratified LD score regression as used in this manuscript for cell-type-speciifc analyses, we also compared to “unadjusted” stratified LD score regression; i.e., LD score regression used to test for enrichment in total proportion of heritability, not controlling for other methods, in a way analogous to the top SNPs and PICS methods. As expected, this unadjusted version had a high rejection rate both for null baseline enrichment as well as for true cell-type-specific signal, for the same reasons that the top SNPs and PICS methods did.
