Fig. 3

Human-inserted and mouse-deleted promoters are enriched for molecular QTL that regulate gene expression. a–c Log2-transformed odds ratios of genomic overlap of promoters with distinct evolutionary histories relative to promoters conserved between human and mouse for a range of molecular QTL. Odds ratios above 0 indicate a greater rate of QTL relative to conserved promoters. Vertical lines indicate the estimate of the odds ratio while horizontal lines show the 95% confidence interval (Fisher’s exact test). The number of promoters overlapping each class of molecular QTL are shown in parentheses. d Heatmap of beta-coefficients from multivariate regression considering evolutionary history and additional promoter and gene features (x-axis). Molecular QTL (y-axis) ordered as in a–c. Red denotes QTL enrichment relative to conserved promoters and grey depletion. Non-significant (p > 0.05) associations have beta rounded to zero (displayed as white). e Spatial enrichment of molecular QTL around promoters when stratified by evolutionary history. Enrichments are plotted as the 250 bp rolling average relative to the 2–4 kb flank upstream from the TSS (arrow). 95% bootstrap confidence intervals are indicated by light outer curves. f Example QTL (reference SNP identifier rs2808385) for H3K27ac RPKM showing a negative derived beta coefficient. g Distribution of derived beta coefficients for all significant H3K27ac QTL overlapping each indicated promoter class