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    LOC112163681 BRD4-independent group 4 enhancer GRCh37_chr14:100863901-100865100 [ Homo sapiens (human) ]

    Gene ID: 112163681, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC112163681
    Gene description
    BRD4-independent group 4 enhancer GRCh37_chr14:100863901-100865100
    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. It 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. This sequence 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 a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Aug 2022]
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    Genomic context

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    Location:
    14q
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (100397564..100398763)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (94630327..94631526)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (100864429..100864723)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9038 Neighboring gene solute carrier family 25 member 47 Neighboring gene tryptophanyl-tRNA synthetase 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100837597-100838513 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9039 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9040 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6090 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6091 Neighboring gene NADH:ubiquinone oxidoreductase subunit B3 pseudogene 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100848141-100849101 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100849328-100849837 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100860083-100860587 Neighboring gene WD repeat domain 25 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100870227-100870728 Neighboring gene uncharacterized LOC105370664 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:100876203-100876704 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:100876705-100877204 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100885967-100886468 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100886469-100886968 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100893614-100894278 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:100904917-100906116 Neighboring gene Sharpr-MPRA regulatory region 12420 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100913795-100914295 Neighboring gene uncharacterized LOC124903383

    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

    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

    • Sharpr-MPRA regulatory region 10653

    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_056656.2 

      Range
      101..1300
      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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      100397564..100398763
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      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      94630327..94631526
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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