Genome browser track showing the confidence interval of inversion breakpoints and annotated TAD boundaries 73 around them. Below, NO differences at CREs between Xq-Inv and WT cells are shown as log 2 -fold changes (permutation-adjusted P values computed using a sliding window approach 20 ). The most significant signal out of 13 peaks representing patterns of haplotype-specific NO is a region with inferred increased chromatin accessibility, which overlaps with annotated AR enhancers 74 residing 386 kb apart from the AR gene. Three annotated AR enhancers intersecting with the most significant peak are highlighted in red. The black vertical dotted lines indicate the breakpoint positions of mSVs, and the red horizontal dotted lines show the significance level of haplotype-specific NO (FDR 5%, and 10%).
