We used LDSC (LD SCore, v1.0.0) regression analysis25 to estimate heritability of AD and schizophrenia from GWAS summary statistics (excluding the APOE [chr19:45000000–45800000] and MHC/HLA [chr6:28477797–33448354] regions) partitioned by PU.1 ChIP-Seq binding sites in myeloid cells, as described in the companion website (see URLs) and controlling for the 53 functional annotation categories of the full baseline model. GWAS summary statistics for ADand schizophrenia (SCZ) were downloaded from the IGAP consortium1 (stage 1 dataset) and the Psychiatric Genomics Consortium (PGC)26 (pgc.cross.scz dataset), respectively (see URLs). SPI1 (PU.1) bindings sites were downloaded as filtered and merged ChIP-Seq peaks in BED format from the ReMap database77 (GEO:GSE31621, SPI1, blood monocyte and macrophage datasets35). SPI1 (PU.1) and POLR2AphosphoS5 binding sites were downloaded as broad ChIP-Seq peaks in BED format from the Encode portal7837 (DCC:ENCSR037HRJ; GEO:GSE30567; HL60 dataset) (see URLs).
