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    LOC126861133 MED14-independent group 3 enhancer GRCh37_chr11:8703769-8704968 [ Homo sapiens (human) ]

    Gene ID: 126861133, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC126861133
    Gene description
    MED14-independent group 3 enhancer GRCh37_chr11:8703769-8704968
    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 enhancers that were validated by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA). In HCT116 colorectal carcinoma cells, a subregion was defined as a group 3 enhancer that depends on the BRD2, BRD4, P300/CBP and CDK7 cofactors, but it has limited or no dependence on the MED14 core Mediator complex subunit. Another subregion was also validated as an enhancer by ChIP-STARR-seq in primed human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. This locus also includes three accessible chromatin subregions, two 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 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 LOC126861133 in Genome Data Viewer
    Location:
    chromosome: 11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (8682222..8683713)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (8763976..8765467)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376536 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8271693-8272438 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8272439-8273182 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8281879-8282380 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8283311-8283850 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3113 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:8288990-8289574 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:8289575-8290158 Neighboring gene MPRA-validated peak1191 silencer Neighboring gene LIM domain only 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8303849-8304410 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:8304411-8304972 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8339910-8340410 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:8347375-8347960 Neighboring gene Sharpr-MPRA regulatory region 11418 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8358075-8358892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8359711-8360526 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8360626-8361287 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4382 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4383 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8373273-8373772 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4384 Neighboring gene serine/threonine kinase 33 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4385 Neighboring gene small Cajal body-specific RNA 20 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4386 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3114 Neighboring gene NANOG hESC enhancer GRCh37_chr11:8625413-8625914 Neighboring gene tripartite motif containing 66 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:8692389-8692996 Neighboring gene small nucleolar RNA, H/ACA box 3A Neighboring gene small nucleolar RNA, H/ACA box 3B Neighboring gene ribosomal protein L27a

    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 4387
    • ATAC-STARR-seq lymphoblastoid active region 4388
    • ATAC-STARR-seq lymphoblastoid silent region 3115
    • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:8704618-8705260

    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_085632.2 

      Range
      101..1592
      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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      8682222..8683713
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      8763976..8765467
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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