We downloaded 513 public binary SEG annotations for EUR SNPs from phase 3 of 1000 Genomes53, indicating SNP membership to a 100-kb window around the gene body from the corresponding gene set52. We downloaded 220 public binary CTS annotations of peak data and then annotated EUR SNPs from phase 3 of 1000 Genomes to indicate binary membership to a histone mark peak3. We also acquired the corresponding SEG and CTS SNP-level annotations for EAS SNPs from phase 3 of 1000 Genomes from a previous study24. We then computed LD scores with S-LDSC and partitioned heritability using a customized version of the baseline-LD.
