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LOC126859902 BRD4-independent group 4 enhancer GRCh37_chr6:168681558-168682757 [ Homo sapiens (human) ]

Gene ID: 126859902, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126859902
Gene description
BRD4-independent group 4 enhancer GRCh37_chr6:168681558-168682757
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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 H3K4me1 histone modification were also shown to be active enhancers by ChIP-STARR-seq in primed human embryonic stem cells. An accessible chromatin subregion was used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. That subregion was identified as a functional silencer in K562 erythroleukemia cells. [provided by RefSeq, Jun 2023]
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Genomic context

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Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (168280255..168282077)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (169624412..169626234)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901501 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:168631271-168631772 Neighboring gene uncharacterized LOC101929420 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:168648577-168649077 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:168673827-168674539 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:168679626-168680280 Neighboring gene CTAGE family member 13, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:168694196-168694696 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:168701344-168702332 Neighboring gene dishevelled binding antagonist of beta catenin 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:168703229-168703483 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:168710364-168711351 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:168713461-168714385 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:168714386-168715311

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. Systematic identification of silencers in human cells. Pang B, et al. Nat Genet, 2020 Mar. PMID 32094911, Free PMC Article
  2. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, 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

  • H3K4me1 hESC enhancer GRCh37_chr6:168680935-168681589
  • H3K4me1 hESC enhancer GRCh37_chr6:168681590-168682243
  • ReSE screen-validated silencer GRCh37_chr6:168682209-168682393

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_084403.2 

    Range
    101..1923
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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
    168280255..168282077
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    169624412..169626234
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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