DNase Clusters item details
  Items in Cluster: 95 of 95
Cluster Score (out of 1000): 1000
Position: chr1:175023401-175023610
Band: 1q25.1
Genomic Size: 210
View DNA for this feature (hg38/Human)

List of Items in Cluster
 
#signalcellTypetreatmentmore info
1562.00A549 wgEncodeRegDnaseUwA549Peak
2239.00AG04449 wgEncodeRegDnaseUwAg04449Peak
3452.00AG04450 wgEncodeRegDnaseUwAg04450Peak
4399.00AG09309 wgEncodeRegDnaseUwAg09309Peak
5524.00AG09319 wgEncodeRegDnaseUwAg09319Peak
6574.00AG10803 wgEncodeRegDnaseUwAg10803Peak
7652.00AoAF wgEncodeRegDnaseUwAoafPeak
81241.00BE2_C wgEncodeRegDnaseUwBe2cPeak
9394.00BJ wgEncodeRegDnaseUwBjPeak
10638.00bone_marrow_MSC wgEncodeRegDnaseUwBonemarrowmscPeak
111996.00Caco-2 wgEncodeRegDnaseUwCaco2Peak
124892.00CD20+_RO01778 wgEncodeRegDnaseUwCd20ro01778Peak
13280.00GM04503 wgEncodeRegDnaseUwGm04503Peak
14538.00GM04504 wgEncodeRegDnaseUwGm04504Peak
15974.00GM06990 wgEncodeRegDnaseUwGm06990Peak
161172.00GM12865 wgEncodeRegDnaseUwGm12865Peak
17336.00GM12878 wgEncodeRegDnaseUwGm12878Peak
18796.00H7-hESC wgEncodeRegDnaseUwH7hescPeak
19874.00H7-hESC diffProtA_14d wgEncodeRegDnaseUwH7hescDiffprota14dPeak
20515.00H7-hESC diffProtA_5d wgEncodeRegDnaseUwH7hescDiffprota5dPeak
21221.00HA-h wgEncodeRegDnaseUwHahPeak
22191.00HA-sp wgEncodeRegDnaseUwHaspPeak
23411.00HAc wgEncodeRegDnaseUwHacPeak
24599.00HAEpiC wgEncodeRegDnaseUwHaepicPeak
25459.00HBMEC wgEncodeRegDnaseUwHbmecPeak
26336.00HBVSMC wgEncodeRegDnaseUwHbvsmcPeak
27705.00HCF wgEncodeRegDnaseUwHcfPeak
28252.00HCFaa wgEncodeRegDnaseUwHcfaaPeak
29629.00HCM wgEncodeRegDnaseUwHcmPeak
30692.00HConF wgEncodeRegDnaseUwHconfPeak
31690.00HCPEpiC wgEncodeRegDnaseUwHcpepicPeak
32644.00HCT-116 wgEncodeRegDnaseUwHct116Peak
33387.00HEEpiC wgEncodeRegDnaseUwHeepicPeak
34414.00HeLa-S3 wgEncodeRegDnaseUwHelas3Peak
35764.00HepG2 wgEncodeRegDnaseUwHepg2Peak
36521.00HFF wgEncodeRegDnaseUwHffPeak
37362.00HFF-Myc wgEncodeRegDnaseUwHffmycPeak
38427.00HGF wgEncodeRegDnaseUwHgfPeak
39332.00HIPEpiC wgEncodeRegDnaseUwHipepicPeak
40396.00HL-60 wgEncodeRegDnaseUwHl60Peak
41385.00HMEC wgEncodeRegDnaseUwHmecPeak
42767.00HMF wgEncodeRegDnaseUwHmfPeak
43183.00HMVEC-dAd wgEncodeRegDnaseUwHmvecdadPeak
44897.00HMVEC-dBl-Ad wgEncodeRegDnaseUwHmvecdbladPeak
45835.00HMVEC-dBl-Neo wgEncodeRegDnaseUwHmvecdblneoPeak
46933.00HMVEC-dLy-Ad wgEncodeRegDnaseUwHmvecdlyadPeak
47686.00HMVEC-dLy-Neo wgEncodeRegDnaseUwHmvecdlyneoPeak
48684.00HMVEC-dNeo wgEncodeRegDnaseUwHmvecdneoPeak
49569.00HMVEC-LBl wgEncodeRegDnaseUwHmveclblPeak
50968.00HMVEC-LLy wgEncodeRegDnaseUwHmvecllyPeak
51297.00HNPCEpiC wgEncodeRegDnaseUwHnpcepicPeak
521143.00HPAF wgEncodeRegDnaseUwHpafPeak
53586.00HPdLF wgEncodeRegDnaseUwHpdlfPeak
541121.00HPF wgEncodeRegDnaseUwHpfPeak
55290.00HRCEpiC wgEncodeRegDnaseUwHrcepicPeak
56224.00HRE wgEncodeRegDnaseUwHrePeak
57227.00HRGEC wgEncodeRegDnaseUwHrgecPeak
58364.00HRPEpiC wgEncodeRegDnaseUwHrpepicPeak
59403.00HSMM wgEncodeRegDnaseUwHsmmPeak
60329.00HSMMtube wgEncodeRegDnaseUwHsmmtubePeak
61242.00HUVEC wgEncodeRegDnaseUwHuvecPeak
62400.00HVMF wgEncodeRegDnaseUwHvmfPeak
631435.00Jurkat wgEncodeRegDnaseUwJurkatPeak
64427.00K562 wgEncodeRegDnaseUwK562Peak
65405.00LHCN-M2 wgEncodeRegDnaseUwLhcnm2Peak
66594.00LHCN-M2 DIFF_4d wgEncodeRegDnaseUwLhcnm2Diff4dPeak
67364.00LNCaP wgEncodeRegDnaseUwLncapPeak
68775.00M059J wgEncodeRegDnaseUwM059jPeak
69671.00MCF-7 wgEncodeRegDnaseUwMcf7Peak
701430.00MCF-7 Estradiol_100nM_1hr wgEncodeRegDnaseUwMcf7Estradiol100nm1hrPeak
711380.00MCF-7 Estradiol_ctrl_0hr wgEncodeRegDnaseUwMcf7Estradiolctrl0hrPeak
721222.00Monocytes-CD14+_RO01746 wgEncodeRegDnaseUwMonocytescd14ro01746Peak
73650.00NB4 wgEncodeRegDnaseUwNb4Peak
74305.00NH-A wgEncodeRegDnaseUwNhaPeak
75338.00NHBE_RA wgEncodeRegDnaseUwNhberaPeak
76724.00NHDF-Ad wgEncodeRegDnaseUwNhdfadPeak
77736.00NHDF-neo wgEncodeRegDnaseUwNhdfneoPeak
78139.00NHEK wgEncodeRegDnaseUwNhekPeak
79366.00NHLF wgEncodeRegDnaseUwNhlfPeak
80438.00NT2-D1 wgEncodeRegDnaseUwNt2d1Peak
81259.00PANC-1 wgEncodeRegDnaseUwPanc1Peak
82237.00PrEC wgEncodeRegDnaseUwPrecPeak
83567.00RPMI-7951 wgEncodeRegDnaseUwRpmi7951Peak
84285.00RPTEC wgEncodeRegDnaseUwRptecPeak
85202.00SAEC wgEncodeRegDnaseUwSaecPeak
86237.00SK-N-MC wgEncodeRegDnaseUwSknmcPeak
871481.00SK-N-SH_RA wgEncodeRegDnaseUwSknshraPeak
88725.00SKMC wgEncodeRegDnaseUwSkmcPeak
891702.00T-47D wgEncodeRegDnaseUwT47dPeak
901566.00Th1 wgEncodeRegDnaseUwTh1Peak
91514.00Th1_Wb54553204 wgEncodeRegDnaseUwTh1wb54553204Peak
92972.00Th2 wgEncodeRegDnaseUwTh2Peak
93607.00WERI-Rb-1 wgEncodeRegDnaseUwWerirb1Peak
94443.00WI-38 wgEncodeRegDnaseUwWi38Peak
95213.00WI-38 4OHTAM_20nM_72hr wgEncodeRegDnaseUwWi384ohtam20nm72hrPeak
List all items assayed

Track Description
 
View table: schema,

Go to DNase Clusters track controls

Data last updated: 2019-01-08


p12 Note: includes annotations on GRCh38.p12 patch sequences

Description

This track shows clusters of DNaseI hypersensitivity derived from assays in 95 cell types by the John Stamatoyannapoulos lab at the University of Washington from September 2007 to January 2011, as part of the ENCODE project first production phase. Regulatory regions in general, and promoters in particular, tend to be DNase-sensitive.

Additional views of this data sites are displayed from the DNaseI HS track. The peaks in that track are the basis for the clusters shown here, which combine data from peaks from the different cell lines. Please note that track colors for the DNase tracks are based on similiarity of cell types, while there is different coloring for cell types on the ENCODE hg38 Transcription track, Layered H3K4Me1 track, Layered H3K4Me3 track, and Layered H3K27Ac track, which match the coloring used in their previous versions lifted from the hg19 assembly.

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 1-1000 (where score is based on signal strength).

Methods

Raw sequence data files were processed by the UCSC ENCODE DNase analysis pipeline (July 2014 specification), diagrammed here:

ENCODE DNase Pipeline Credit: Qian Alvin Qin, X. Liu lab

Briefly, sequence files were aligned to the hg38 (GRCh38) genome assembly augmented with 'sponge' sequence (ref). Multi-mapped reads were removed, as were reads that aligned to 'sponge' or mitochondiral sequence. Results from all replicates were pooled, and further processed by the Hotspot program to call peaks.

Peaks of DNaseI hypersensitivity from the ENCODE DNase Analysis Pipeline at UCSC 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. Additional documentation on the methods used to identify hypersensitive sites are available from the DNaseI HS track.

Credits

This track is based on sequence data from the University of Washington ENCODE group, with subsequent processing by UCSC. For additional credits and references, see the DNaseI HS track.