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Super Enhancer Details

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General details

Super-Enhancer ID: SE_00063
Genomic locus: chr3:42053210-42165022
Size/Length: 111812 bp
Genome: Human - hg19
Cell/Tissue: Adipose Nuclei
Factor(s) Used: H3K27ac - (Used to define enhancers)
H3K27ac - (Used to rank SEs)
Input/WCE: GSM621401
Reference: Hnisz D. et al., 2013 Cell - 24119843

Associated gene details

RefSeq ID: NM_001042646
Gene Symbol: TRAK1
Chromosome: chr3
TSS: 42201660 (Transcription start site)
TES: 42254118 (Transcription end site)
Strand: +
Number of Exons: 13
External Links:

Software and parameters used

Read Mapping: Bowtie (version 0.12.9) with parameters -k 2, -m 2, -n 2, -best.
Peak Calling: MACS (version 1.4.1) with parameters -p 1e-9,-keep-dup = auto, -w -S -space = 50
Stitching Distance: 12.5 kb
TSS Exclusive Zone: +/- 2 kb
Enhancer-gene Assignment: Genes were assigned to SEs within a 50 kb window. In cases where experimentally verified enhancer-gene assignments were available, genes were assigned to enhancers based on those studies.

FASTA sequence



>chr3:42053210-42165022
Sequence preview unavailable; use Download FASTA.

Wiggle files

Download Wiggle (WIG) files, generated by original data source.

Constituents of Super-enhancer - SE_00063

Constituent ID SE ID Chrom Start End Constituent Size MACS score
C004073 SE_00063 chr3 42053210 42058517 5307 2188.36
C004074 SE_00063 chr3 42060660 42068971 8311 3100
C004075 SE_00063 chr3 42073059 42080252 7193 3100
C004076 SE_00063 chr3 42083844 42085337 1493 429.38
C004077 SE_00063 chr3 42085462 42086940 1478 260.78
C004078 SE_00063 chr3 42092425 42097420 4995 2884
C004079 SE_00063 chr3 42100849 42110891 10042 3100
C004080 SE_00063 chr3 42111769 42116338 4569 3100
C004081 SE_00063 chr3 42119016 42120297 1281 126.95
C004082 SE_00063 chr3 42120704 42125360 4656 3100
C004083 SE_00063 chr3 42131608 42135031 3423 2997.98
C004084 SE_00063 chr3 42135227 42136785 1558 218.3
C004085 SE_00063 chr3 42138563 42145096 6533 2977.5
C004086 SE_00063 chr3 42156150 42161441 5291 2439.2
C004087 SE_00063 chr3 42163642 42165022 1380 105.94