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LOC126862882 BRD4-independent group 4 enhancer GRCh37_chr19:19599635-19600834 [ Homo sapiens (human) ]

Gene ID: 126862882, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126862882
Gene description
BRD4-independent group 4 enhancer GRCh37_chr19:19599635-19600834
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). 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 were also shown to be active enhancers by ChIP-STARR-seq in primed human embryonic stem cells, where both are marked by the H3K27ac and H3K4me1 histone modifications and one is additionally associated with the OCT4 and NANOG transcription factors. 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 LOC126862882 in Genome Data Viewer
Location:
chromosome: 19
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (19488176..19490025)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (19625659..19627508)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene MAU2 sister chromatid cohesion factor Neighboring gene uncharacterized LOC124904656 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14347 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14348 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14349 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr19:19481673-19482872 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19489171-19489816 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10439 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14350 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19505798-19506651 Neighboring gene GATA zinc finger domain containing 2A Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr19:19515640-19516548 and GRCh37_chr19:19516549-19517455 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14352 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14353 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19538881-19539384 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19546839-19547444 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14354 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19563343-19563843 Neighboring gene microRNA 640 Neighboring gene Sharpr-MPRA regulatory region 5941 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14356 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14357 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19573083-19573864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19583474-19584166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19584167-19584858 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10444 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19585552-19586243 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19593349-19593956 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19595063-19595847 Neighboring gene Sharpr-MPRA regulatory region 10818/8147 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:19602420-19603619 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19615802-19616302 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10445 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14360 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19635662-19636637 Neighboring gene Sharpr-MPRA regulatory region 9511 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19638979-19639479 Neighboring gene NADH:ubiquinone oxidoreductase subunit A13 Neighboring gene testis specific serine kinase 6

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 14358
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19598985-19599768
  • OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19599769-19600552

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_087379.2 

    Range
    101..1950
    Download
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    19488176..19490025
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    19625659..19627508
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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