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LOC126807599 BRD4-independent group 4 enhancer GRCh37_chr5:171788418-171789617 [ Homo sapiens (human) ]

Gene ID: 126807599, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126807599
Gene description
BRD4-independent group 4 enhancer GRCh37_chr5:171788418-171789617
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 region was validated as an active enhancer by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in HCT116 colorectal carcinoma cells, where it 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. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (172361414..172362613)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (172901656..172902855)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ubiquitin domain containing 2 Neighboring gene KLF3 pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:171710845-171711445 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:171711446-171712045 Neighboring gene uncharacterized LOC100288254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23633 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23634 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:171762901-171763762 Neighboring gene SH3 and PX domains 2B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23636 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16621 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23637 Neighboring gene MPRA-validated peak5578 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:171839705-171840206 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:171845006-171845982 Neighboring gene Sharpr-MPRA regulatory region 10478 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:171858257-171858757 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:171859347-171859604 Neighboring gene Sharpr-MPRA regulatory region 6627 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:171880495-171881016 Neighboring gene uncharacterized LOC105377727 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:171906087-171906708 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:171906709-171907328 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:171911421-171911922 Neighboring gene uncharacterized LOC107984004 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23638 Neighboring gene Sharpr-MPRA regulatory region 3838 Neighboring gene long intergenic non-protein coding RNA 1944

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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 23635

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_083913.1 

    Range
    101..1300
    Download
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    172361414..172362613
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    172901656..172902855
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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