a Overall schematic of experiment b. DNase-seq profiles at the Pparg locus in liver, kidney, lung tissue, and B cells from F1 crosses of C57Bl/6J dams with 129/SvImJ and CAST/EiJ sires. c Fragment length distribution of samples showing high-quality libraries comprising non-nucleosomal fragments. d Hierarchical clustering of DHSs from high-depth samples. e–f Counts of SNVs shared across strains (e) and cell types (f). g Counts of imbalanced SNVs (FDR 10%). Counts are reported in aggregate across all data sets (left), by cell type (middle), and by parental strain (right). h Summary of the master list of DHSs overlapping SNVs from all strains. Counts include all DHSs (dark gray), DHSs with SNVs (light gray), DHSs passing mappability filters (orange), DHSs with sufficient coverage to test for imbalance across all data sets (green) and in individual cell types or strains (blue). Counts include only autosomal DHSs. i Pearson correlation of allelic ratios at adjacent SNVs broken down by distance to next SNV. The dashed line represents the median width of DHS hotspots overlapping SNVs in this study.