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LOC112694696 BRD4-independent group 4 enhancer GRCh37_chr20:25218064-25219263 [ Homo sapiens (human) ]

Gene ID: 112694696, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112694696
Gene description
BRD4-independent group 4 enhancer GRCh37_chr20:25218064-25219263
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. A subregion 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. A subregion was also validated as an enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). Another subregion was also validated as an enhancer by ChIP-STARR-seq in primed human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
20p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (25237327..25238627)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (25302292..25303592)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (25218469..25218763)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 10160 Neighboring gene NIPAL1 pseudogene 1 Neighboring gene uncharacterized LOC101926889 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17660 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12741 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17661 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17662 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17663 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:25194425-25194926 Neighboring gene ectonucleoside triphosphate diphosphohydrolase 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25202205-25202966 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25202967-25203726 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25203727-25204488 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:25204539-25204720 Neighboring gene uncharacterized LOC105372579 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17664 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12742 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr20:25222455-25223072 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12744 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12743 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:25227753-25228006 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12745 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17665 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12746 Neighboring gene glycogen phosphorylase B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:25274716-25275238 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:25276284-25276805 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:25280703-25281254 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:25281255-25281805 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:25289826-25291025 Neighboring gene abhydrolase domain containing 12, lysophospholipase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:25297613-25298222 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17667 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17668 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12747 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:25310906-25311427 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25337131-25337731 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25337732-25338331 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12748 Neighboring gene peptidylprolyl isomerase A pseudogene 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. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, Free PMC Article
  2. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25217963-25218739
  • Sharpr-MPRA regulatory region 4288

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_060726.3 

    Range
    101..1401
    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    25237327..25238627
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    25302292..25303592
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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