All S-LDSC analyses used LD scores computed from in-sample summary LD information (based on imputed SNP dosages rather than sequenced genotypes as in previous publications24–26, assigning to each SNP the LD score computed in the locus in which it was most central) because they provide better coverage of low-frequency SNPs and are consistent with the fine-mapping analyses. We computed genetic correlations with LDSC, using the same summary statistics used for fine-mapping and restricting the analysis to common SNPs.
