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LOC126861537 BRD4-independent group 4 enhancer GRCh37_chr12:56817170-56818369 [ Homo sapiens (human) ]

Gene ID: 126861537, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126861537
Gene description
BRD4-independent group 4 enhancer GRCh37_chr12:56817170-56818369
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 was validated as an active enhancer by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay 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. 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 HepG2 liver carcinoma cells. [provided by RefSeq, Jun 2023]
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Genomic context

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Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (56423386..56424585)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (56391102..56392301)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene TBCC domain containing 1 pseudogene Neighboring gene apolipoprotein N, pseudogene Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:56795121-56795653 Neighboring gene timeless circadian regulator Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:56837017-56837650 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:56842091-56842611 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6496 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6497 Neighboring gene major intrinsic protein of lens fiber Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6498 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6499 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6500 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6501 Neighboring gene SPRY domain containing 4 Neighboring gene glutaminase 2

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

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

  • ReSE screen-validated silencer GRCh37_chr12:56817182-56817429

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_086036.1 

    Range
    101..1300
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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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    56423386..56424585
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    56391102..56392301
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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