possible SNP-pairs in LD (r2 > 0.1) and/or within < 1 Mb distance of each other (Supplementary Methods). Then, boundaries of the most distal SNP on either side around lead SNPs (r2 > 0.5) were used as criteria to list genes from SNPs, from which potential enrichment of these genes to specific cell types could later be assessed. By comparing cell type enrichment results of LDSC, DEPICT, and MAGMA, we evaluated the relative stringency of each method. This was accomplished by comparing the P values, denoting the strength of association of a given cell type with a given phenotype, of any two methods with one another.
