Fig. 2: Identification and characterization of candidate CREs across mouse cerebral cell types.

a, Pie chart showing the fraction of cCREs that overlaps with different classes of annotated sequences in the mouse genome. TSS, transcription start site; TTS, transcription termination site. b, Venn diagram showing the overlap between cCREs defined in this study (in red) and the DHSs in the SCREEN database (in grey)¹⁴. c, Box plots showing sequence conservation measured by PhastCons score⁵⁹. ***P < 0.001, Wilcoxon rank-sum test. Boxes span the first to third quartiles (Q1 to Q3), horizontal line denotes the median, and whiskers show 1.5× the interquartile range (IQR). d, Bar chart showing the fold enrichment of cCREs within the different states of mouse brain chromatin³¹ annotated with a 15-state ChromHMM model³³. e, Density map comparing the median and maximum variation of chromatin accessibility at each cCRE across cell types. Each dot represents a cCRE. Red box highlights elements with low chromatin accessibility variability across clusters. f, Stacked bar plot showing the fraction of cCREs with low variability overlapping with distinct genomic features. g, Heat map showing association of the 43 subclasses (rows) with 42 cis-regulatory modules (top, from left to right). Columns represent cCREs. A full list of subclass or module associations is in Supplementary Table 9, and the association of cCREs to modules is in Supplementary Table 10. CPM, counts per million.