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LOC126859769 BRD4-independent group 4 enhancer GRCh37_chr6:115322458-115323657 [ Homo sapiens (human) ]

Gene ID: 126859769, updated on 12-Sep-2024

Summary

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Gene symbol
LOC126859769
Gene description
BRD4-independent group 4 enhancer GRCh37_chr6:115322458-115323657
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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See LOC126859769 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (115001294..115002493)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (116184552..116185751)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (115322458..115323657)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene lncRNA periodontal mesenchymal stem cell osteogenesis related Neighboring gene NANOG hESC enhancer GRCh37_chr6:114885549-114886071 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:115046932-115047452 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:115047453-115047971 Neighboring gene RNA, U6 small nuclear 475, pseudogene Neighboring gene uncharacterized LOC107986639 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24974 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:115352812-115353362 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:115358194-115358741 Neighboring gene uncharacterized LOC105377960 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:115391597-115392796 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_87752 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:115571209-115571710 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:115571711-115572210 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:115735940-115736652 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:115736653-115737364 Neighboring gene uncharacterized LOC105377961

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 within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. 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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 24975

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_084270.1 

    Range
    101..1300
    Download
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    115001294..115002493
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    116184552..116185751
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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