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LOC126862004 BRD4-independent group 4 enhancer GRCh37_chr14:77370757-77371956 [ Homo sapiens (human) ]

Gene ID: 126862004, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126862004
Gene description
BRD4-independent group 4 enhancer GRCh37_chr14:77370757-77371956
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 (MPRA). In HCT116 colorectal carcinoma cells, a subregion 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. Another subregion was also validated as an enhancer by ChIP-STARR-seq in naive human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. 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: 14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (76903851..76905613)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (71113571..71115334)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene ribosomal protein L22 pseudogene 2 Neighboring gene RN7SK pseudogene 17 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8774 Neighboring gene Sharpr-MPRA regulatory region 8364 Neighboring gene VISTA enhancer hs1466 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:77389998-77390993 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:77390994-77391988 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:77393097-77394053 Neighboring gene uncharacterized LOC124903349 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr14:77401173-77401771 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr14:77401772-77402369 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:77406282-77406782 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8776 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:77419449-77420018 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:77420019-77420588 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8777 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:77422669-77423203 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8778 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8779 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:77426954-77427488 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:77427489-77428024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8781 Neighboring gene Sharpr-MPRA regulatory region 14350 Neighboring gene long intergenic non-protein coding RNA 1629

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
  3. 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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 8773
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:77370194-77370931

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_086502.2 

    Range
    101..1863
    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    76903851..76905613
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    71113571..71115334
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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