a, GO enrichment of genes that change compartment status from A to B (left) and B to A (right) in GZ to CP. b, Heat map of PC1 values of the genome that change compartment status in different cell types. The faction of the genome with a compartment switch in different lineages is described below. c, Distribution of gene expression fold change (FC, left) and DHS FC (right) for genes/regions that change compartment status (‘A to B’ or ‘B to A’) or that remain the same (stable) in different cell/tissue types. B to A compartment shift is associated with increased DHS and gene expression, whereas the A to B shift is associated with decreased DHS and gene expression. P values from one-way ANOVA; whiskers, 1.5 × interquartile range (IQR); centre lines, median (black) and mean (grey). d, Percentage of epigenetic states for genomic regions that change compartment status between ES cells and GZ (left) and ES cells and CP (right). Note that B to A shift in ES cells to GZ/CP is associated with increased proportion of active promoter and transcribed regions (TssA and Tx) and enhancers (Enh, top), while A to B shift in ES cells to GZ/CP is associated with increased proportions of repressive marks (Het and ReprPCWk, bottom). *P < 0.05, **P < 0.01, ***P < 0.001. P values from Fisher’s test. Annotation for epigenetic marks described in a core 15-state model from ref. 33. e, Epigenetic changes in TADs mediate gene expression changes during neuronal differentiation. Genes were divided by expression FC between ES and differentiated neural cells, and epigenetic states in the TADs containing genes in each group were counted and compared between ES cells and CP. Upregulated genes in neurons reside in TADs with more active epigenetic marks in CP than in ES cells, while downregulated genes in neurons reside in TADs with more repressive marks in CP than in ES cells. Epigenetic states associated with activation and transcription of the genes were marked as red bars, while those associated with repression were marked as blue bars on the right. Annotation for epigenetic states described in ref. 33. f, Histone mark enrichment for adult cortical eQTL in fetal brain (FB, left) and adult frontal cortex (FCTX, right). g, Hi-C interaction frequency between eQTL and associated transcripts. LOESS smooth curve plotted with actual data points. Shaded area corresponds to 95% confidence intervals. GZ, chromatin contact frequency in GZ; ES, chromatin contact frequency in ES cells; Exp, expected interaction frequency given the distance between two regions; Opp, opposite interaction frequency: interaction frequency of SNPs and transcripts when the position of genes was mirrored relative to the eQTL. ***P < 0.001, P values from repeated measure of ANOVA.