(B) Spearman correlations between libraries across variables. The notches describe the 95% confidence interval of the median. ‘Across cell’ indicates comparisons between libraries which are from the same individual and treatment, but different cell types. ‘Across individual’ indicates comparisons between libraries from the same cell type, treatment, and replicate (i.e. plate), but different individuals. ‘Across replicate’ indicates comparisons between libraries from the same cell type, treatment, and individual, but different replicates (i.e. plate). ‘Across treatment’ indicates comparisons between libraries which are from the same cell type, individual, and replicate (i.e. plate), but different treatments. ‘Control1 vs Control2’ indicates comparisons between the two vehicle controls from the same individual and replicate (i.e. plate). (C) QQ-plot depicting interaction -values for SNPs tested for cASE. G×C indicates SNPs tested for GenexCell type effects, G×T indicates SNPs tested for Gene × treatment effects, G×C×T indicates genes tested for Gene × cell type × treatment effects. Ctr1 vs Ctr2 indicates the coefficient in the model that accounts for the vehicle control used for each treatment. (D) Number of treatment G×E. Gene × treatment and gene × treatment × cell type cASE is reported for each treatment, irrespective of the cell type in which it was identified. (E) Enrichment of genes with ASE and treatment cASE in eGenes from large ASE/eQTL mapping studies: (1,2) CMs in GTEx heart tissues ASE/eQTL (left ventricle, LV and atrial appendage, AA), (3) IPSCs in i2QTL, (4) LCLs in Geuvadis. Odds ratios and 95% confidence intervals are plotted (Fisher’s test). (F) Gene-by-treatment cASE shared between treatments. For each treatment pair, we calculate the proportion of shared cASE over the union of cASE identified in each of the two treatments (Jaccard Index). (G) Forest plot depicting the significant (FDR <10%) enrichment and depletion of ASE and cASE SNPs with respect to all SNPs tested for different genomic annotations.