a. Relative enrichment or depletion of genomic elements within breakpoint-resolved deletions binned by VAF. TF, transcription factor binding site; nc, noncoding. RVIS range from 0–100 (low <20, medium 20–50, high ≥50). *no element intersected. b. Enrichment/depletion of genomic elements within different SV classes, compared with breakpoint-resolved deletions. c. Manhattan plot of DUSP22-eQTL. Inset: boxplots of association between copy-number genotype and expression. d. Manhattan plot of ZNF43-eQTL. e. Enrichment of SV-containing haplotypes at previously reported GWAS hits (error bars show s.e.m.).