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LOC126861541 BRD4-independent group 4 enhancer GRCh37_chr12:57914069-57915268 [ Homo sapiens (human) ]

Gene ID: 126861541, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126861541
Gene description
BRD4-independent group 4 enhancer GRCh37_chr12:57914069-57915268
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 gene regulatory elements that were validated by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA). 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 H3K27ac and H3K4me1 histone modifications were also shown to be active enhancers by ChIP-STARR-seq in naive and primed human embryonic stem cells. This locus also includes four accessible chromatin subregions, three of which were validated as enhancers and one as a silencer based on their ability to activate or repress an origin of replication minimal core promoter by ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) in GM12878 lymphoblastoid 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 (57520282..57522232)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (57488510..57490460)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene methionyl-tRNA synthetase 1 Neighboring gene uncharacterized LOC128125814 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:57913133-57914094 Neighboring gene microRNA 6758 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57916016-57916975 Neighboring gene DNA damage inducible transcript 3 Neighboring gene microRNA 616 Neighboring gene methyl-CpG binding domain protein 6 Neighboring gene dynactin subunit 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6548 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4584 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57944162-57944754 Neighboring gene kinesin family member 5A Neighboring gene ReSE screen-validated silencer GRCh37_chr12:57955995-57956161 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:57956855-57957072

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 6544
  • ATAC-STARR-seq lymphoblastoid active region 6545
  • ATAC-STARR-seq lymphoblastoid active region 6546
  • ATAC-STARR-seq lymphoblastoid silent region 4582
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57914095-57915054
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57915055-57916015

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_086040.3 

    Range
    101..2051
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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
    57520282..57522232
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    57488510..57490460
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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