Scores were calculated in FinnTwin12 using the score procedure in PLINK version 1.9 (Chang et al., 2015) summing each individual’s total number (imputed dosage) of minor alleles from the score SNPs, with each SNP weighted by the negative log of the GWAS association p value and sign of the association (beta) statistic. As illustrated in Figure 1, identical procedures were used to create a set of DNase I-restricted polygenic scores, except that the final list of LD-pruned SNPs described above was further restricted to SNPs located in DHS sites. The locations of DHSs were based on narrow peak hotspots identified across 53 consolidated epigenomes by the RoadMap Epigenomics Project (http://www.roadmapepigenomics.org). The 53 epigenomes are summarized in the Supplementary Information (Table S1). SNPs were considered to be DHS SNPs if they directly overlapped a DHS or were in perfect linkage disequilibrium (LD) with another SNP overlapping a DHS. Of the 212,718 genome-wide score SNPs, 78,948 (37%) were located in a DHS site, and 3,946 (37%) and 789 (36%) of the DHS score SNPs fell under the GWAS p value thresholds of
