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LOC113146414 BRD4-independent group 4 enhancer GRCh37_chr6:134757040-134758239 [ Homo sapiens (human) ]

Gene ID: 113146414, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113146414
Gene description
BRD4-independent group 4 enhancer GRCh37_chr6:134757040-134758239
Gene type
biological region
Feature type(s)
regulatory: enhancer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as an active enhancer by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay in HCT116 colorectal carcinoma cells. This sequence was defined as a group 4 enhancer that depends on the BRD2, P300/CBP, MED14 and CDK7 cofactors, but it has limited or no dependence on the BRD4 bromodomain protein. A subregion was also validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin), with weak activation in HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Aug 2022]
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Genomic context

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See LOC113146414 in Genome Data Viewer
Location:
6q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (134435902..134437101)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (135624148..135625347)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (134757389..134757683)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378009 Neighboring gene SGK1-CHCHD2P4 intergenic CAGE-defined mid-level expression enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17559 Neighboring gene coiled-coil-helix-coiled-coil-helix domain containing 2 pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25090 Neighboring gene long intergenic non-protein coding RNA 1010 Neighboring gene cancer/testis associated transcript 69 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:134808766-134808977 Neighboring gene long intergenic non-protein coding RNA 3002 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:134855294-134856493 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:134858047-134859246

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, Free PMC Article
  2. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • Sharpr-MPRA regulatory region 14472

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_061642.2 

    Range
    101..1300
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    134435902..134437101
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    135624148..135625347
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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