(A) Cumulative distribution of the distance from the TSS (x-axis) to the nearest site of differential allelic occupancy for all autosomal genes with differential allelic (orange) or equal allelic (blue) expression. (Left) All genes with differential allelic expression, where the difference between the two distributions is highly significant. (Right) Genes with equal allelic expression, and there is no significant difference between the two distributions. (B) Spearman's correlation (y-axis) of allelic occupancy with allelic expression within the distance from autosomal TSSs indicated on the x-axis. For each point, we aggregated all allelic occupancy (both for sites with and without a significant allelic imbalance) at the indicated distance around all genes with significant differential allelic expression. Then, for every gene with at least a single site with a significant differential allelic occupancy, we calculate Spearman's correlation coefficient and plot. Detailed scatter plots are included in Supplemental Figure 20. (C) Differential allelic occupancy of multiple factors at variants either directly or through perfect linkage disequilibrium (R2 = 1; red dash) with celiac disease. Nearby, RMI2 (also known as C16orf75) is predominantly expressed from the maternal allele, and the regulatory interaction is supported by expression quantitative trait loci (eQTL) mapping. (D) Similar to C, allelic occupancy of EBF1 at a variant associated (via linkage disequilibrium) with psoriasis corresponds with differential allelic expression of COG6. Again, the regulatory interaction is supported by eQTL analysis.
