a, b Example DHSs showing cell-type-specific imbalance. Normalized DNaseI cleavage density is colored by signal mapping to reference (blue) and non-reference (red) alleles based on the aggregation of informative SNVs. Counts by peaks denote the sum of reads mapping to reference and non-reference alleles for all SNVs in region; *indicates statistically significant allelic imbalance. Selected TF recognition sequences overlapping imbalanced SNVs are highlighted below. a DHS accessible in liver and lung but with imbalance only in the liver. b. DHSs accessible in all 4 tissues (left) or specific to B cells (right); both DHSs only show an imbalance in B6xCAST and B6xSPRET B cells. c–d Sharing of imbalance by cell type. 1 – π0 represents the proportion of rejected null hypotheses by Storey’s method. c Average sharing of imbalance (1 − π0) between samples of the same cell type vs. samples sharing only the same strain or unrelated samples (sharing neither strain nor cell type). Bar height represents the mean of all pairwise comparisons; error bars represent standard deviation. d. Pairwise sharing of imbalance between cell or tissue types.