Fig. 4

Overlap fine-mapped GWAS variants with sequence-conserved ELEs. For each of the 94 traits, we compute fractions of putative causal SNPs that fall inside the omnibus ELEs (NC) and the sequence-conserved subsets (LC, MC, HC) and then compare them against the fraction of putative causal SNPs among all fine-mapped SNPs in the genome for the trait to assess enrichments. A fine-mapped SNP is “putative causal” for a trait if this SNP has a PIP above a given threshold. a Median fractions and enrichments across 94 traits for 2 fine-mapping methods. b Individual fractions and enrichments for 5 traits based on SUSIE. Additional results are available in Additional file 1: Table S13. c Fractions of SNPs with SUSIE-estimated PIP \(\ge 0.1\) that fall inside HC context-specific ELEs from each of the 17 context groups for 5 traits. The solid and dashed lines denote the fractions of putative causal SNPs for a given trait that fall inside HC omnibus ELEs and the whole genome, respectively. Additional results are available in Additional file 1: Table S14