Extended Data Fig. 6: E–P interaction frequency in active and inactive tissues.

a, The ratio of E–P interaction frequency between active and inactive tissues. b, Univariate logistic regression for relative interaction frequencies and enhancer activity across all tissues. c, The ratio of E–P interaction frequency between active and inactive tissues for interactions within or across TADs. d, The distribution of distances between the closest TAD boundary and enhancer for enhancers acting within or across TADs. e, The ratio of interaction frequency between active and inactive tissues on interacting promoters or intervening regions before and after removing ENCODE annotated elements (±20kb). f, The ratio of E–P interaction frequency between active and inactive tissues for enhancers with different ranks. Only tissues with ≥10 interactions in each rank category are shown. g, The fold-change of gene expression levels between active state (baited enhancers interact with active promoters) and inactive state (baited enhancers don’t interact with promoters or in inactive tissues). Data are represented as mean ± s.e.m. h, The ratio of E–P interaction frequency between active and inactive tissues for expressed genes (TPM>=0.5) and lowly expressed or inactive genes (TPM<0.5). i, Chromatin interaction profiles in forebrain, midbrain and hindbrain centered on the enhancer hs1172 at Nr2f1 locus (chr13:78,057,768–78,705,499). j, The ratio of E–P interaction frequency between active and inactive brain regions for enhancers active in one of the brain domains. k-m, Cumulative frequency plots of inter-probe distances for the indicated loci and tissues. n-p, Frequency distribution of FISH inter-probe distances in 250 nm bins between Zic1/4 and hs654 (n), Mir9–2 and hs266 (o), Snai2 and hs1431 (p) in indicated tissues. P values are calculated by paired-sample (a, c, e, g, h, j) or unpaired-sample (d, f) two-sided Wilcoxon rank test and adjusted for multiple testing or by one-sided chi-squared test (b, n-p). For the boxplots in panels a, c-f, h and j, the central horizontal lines are the median, with the boxes extending from the 25th to the 75th percentiles. The whiskers further extend by ±1.5 times the interquartile range from the limits of each box.