ENCODE Regulation DNase Clusters Track Settings
DNaseI Hypersensitivity Clusters in 125 cell types from ENCODE (V3)

Track collection: Integrated Regulation from ENCODE

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Minimum Display score (0-1000): (100 to 1000)
File Name for downloading:wgEncodeRegDnaseClusteredV3.bed.gz
Data schema/format description and download
Data last updated at UCSC: 2019-01-10


This track shows DNase hypersensitive areas assayed in a large collection of cell types by the ENCODE project. Regulatory regions in general, and promoters in particular, tend to be DNase-sensitive. Additional views of this data and additional documentation on the methods used to identify hypersensitive sites are available from the Uniform DNaseI HS page. The uniform peaks in that track are the basis for the clusters shown here, which combine data from the peaks of the different cell lines.

Display Conventions and Configuration

A gray box indicates the extent of the hypersensitive region. The darkness is proportional to the maximum signal strength observed in any cell line. The number to the left of the box shows how many cell lines are hypersensitive in the region. The track can be configured to restrict the display to elements above a specified score in the range 100-1000 (where score is based on signal strength).


Stringent (FDR 1% thresholded) peaks of DNaseI hypersensitivity from uniform processing by the ENCODE Analysis Working Group (Uniform DNaseI HS) were assigned normalized scores (by UCSC regClusterMakeTableOfTables) in the range 0-1000 based on the narrowPeak signalValue and then clustered on score (by UCSC regCluster) to generate singly-linked clusters. Low-scoring clusters (score <100) were then filtered out.

Release Notes

This is the third release of this track. It differs from the previous track as it includes clusters having only 1 cell type contributing to the cluster (previously excluded). The previous track is available on the UCSC preview browser as DNase Clusters V2.


This track shows data from the University of Washington and Duke ENCODE groups, with uniform processing by the ENCODE Analysis Working Group. The clustering was performed at UCSC. For additional credits and references, see the Uniform DNaseI HS page.

Data Release Policy

While primary ENCODE data is subject to a restriction period as described in the ENCODE data release policy, this restriction does not apply to the integrative analysis results. The data in this track are freely available.