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LOC126860596 BRD4-independent group 4 enhancer GRCh37_chr9:22102887-22104086 [ Homo sapiens (human) ]

Gene ID: 126860596, updated on 12-Sep-2024

Summary

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Gene symbol
LOC126860596
Gene description
BRD4-independent group 4 enhancer GRCh37_chr9:22102887-22104086
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 includes enhancers that were validated by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay. The major subregion had activity 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. Two subregions marked by the H3K27ac histone modification were also shown to be active enhancers by ChIP-STARR-seq in primed human embryonic stem cells. [provided by RefSeq, Nov 2022]
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Genomic context

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See LOC126860596 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (22102608..22104087)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (22116901..22118376)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (22102607..22104086)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19815 Neighboring gene Sharpr-MPRA regulatory region 15403 Neighboring gene CDKN2B antisense RNA 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:22026023-22027222 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28245 Neighboring gene ubiquitin A-52 residue ribosomal protein fusion product 1 pseudogene 6 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 9:22068931 Neighboring gene cyclin dependent kinase inhibitor 2B Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:22117311-22118510 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28246 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:22363678-22364189 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:22446999-22447498 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:22483523-22484150 Neighboring gene DMRT like family A1 Neighboring gene LINE-1 retrotransposable element ORF2 protein-like Neighboring gene long intergenic non-protein coding RNA 1239

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. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

  • H3K27ac hESC enhancer GRCh37_chr9:22102607-22103108
  • H3K27ac hESC enhancer GRCh37_chr9:22103109-22103608

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_085096.2 

    Range
    101..1580
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    22102608..22104087
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    22116901..22118376
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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