Systematic profiling of DNase I hypersensitivity, chromatin states, and gene expression across nine cell types. a Chromatin states and DNase I hypersensitivity density tracks in and around the ABCC8 locus. Human pancreatic islet chromatin states are similar to some of the other ENCODE cell types at the commonly expressed flanking gene NCR3LG1 and unique at the islet-specific expressed gene ABCC8. (Upper) DNase I Hypersensitivity Density Signal from ENCODE/Duke in dense format for each of nine human cell types (islets; GM12878, lymphoblastoid cells; H1 ES, embryonic stem cells; HepG2, hepatocellular carcinoma; HMEC, mammary epithelial cells; HSMM, smooth muscle myoblasts; HUVEC, umbilical vein endothelial cells, K562, erythroleukemia cells, NHEK, keratinocytes). Density graphs (wiggles) of signal enrichment calculated using F-Seq are displayed in grayscale. Scale is from 0 to 0.1. (Middle) ChromHMM-defined chromatin states. Chromatin state assignments are indicated in the top-leftmost key. (Lower) RNA-seq-based expression for each cell type is measured in reads per million mapped reads (RPM) per base pair. Scale is from 0 to 2 for each cell type. Index and tightly linked (r2 ≥ 0.8) SNPs associated with T2D are indicated in green in the T2D GWAS SNPs track and primarily reside in islet-specific SEs. Index SNPs rs5215 and rs5219 are marked with red arrows. The black box highlights a portion of the SE previously shown to direct tissue-specific expression patterns in a spatial and temporal manner in vivo . All processed results are browsable and downloadable at http://research.nhgri.nih.gov/manuscripts/Collins/isletchromatin/. b–d Aggregate DNase-seq tag density (b), H3K27ac ChIP-seq tag density, (c), and (d) CG dinucleotide frequency profiles of 3kbp sequences centered on DNase-seq peak summits—the location of the highest DNase-seq signal—located within SEs or TEs. e DHSs within SEs are much closer together than they are within TEs (two-tailed Wilcoxon rank sum test, p < 10−100 for all cell types). Boxplots show the distance, for each SE or TE DNase-seq summit, to the nearest SE or TE DNase-seq summit, respectively, for all cell types. f DHSs within SEs are moderately longer than DHSs within TEs (two-tailed Wilcoxon rank sum test, p < 10−5 for all cell types). Boxplots show the length of each DHS whose summit overlaps a SE or TE. Boxplot whiskers extend to 1.5× the interquartile range and outliers are shown as block dots, but the y-axis is truncated so that the boxplots can remain in view. Enhancer classes for b–f are indicated in the top-rightmost key.