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LOC126859803 BRD4-independent group 4 enhancer GRCh37_chr6:136610456-136611655 [ Homo sapiens (human) ]

Gene ID: 126859803, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126859803
Gene description
BRD4-independent group 4 enhancer GRCh37_chr6:136610456-136611655
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 primed human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. This locus also includes three accessible chromatin subregions that were validated as enhancers based on their 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: 6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (136289237..136290541)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (137477349..137478653)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene phosphodiesterase 7B Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:136388797-136389341 Neighboring gene PDE7B antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25110 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:136609778-136610374 Neighboring gene uncharacterized LOC124901408 Neighboring gene mitochondrial fission regulator 2 Neighboring gene BCL2 associated transcription factor 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:136655703-136656202 Neighboring gene ribosomal protein lateral stalk subunit P1 pseudogene 8 Neighboring gene MPRA-validated peak6144 silencer Neighboring gene microtubule associated protein 7 Neighboring gene phosphopantothenate--cysteine ligase-like

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 25112
  • ATAC-STARR-seq lymphoblastoid active region 25113
  • ATAC-STARR-seq lymphoblastoid active region 25114
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:136610375-136610971

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_084304.3 

    Range
    101..1405
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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
    136289237..136290541
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    137477349..137478653
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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