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    LOC112163605 H3K4me1 hESC enhancer GRCh37_chr12:52418471-52419408 [ Homo sapiens (human) ]

    Gene ID: 112163605, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC112163605
    Gene description
    H3K4me1 hESC enhancer GRCh37_chr12:52418471-52419408
    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 ChIP-STARR-seq massively parallel reporter assay in primed human embryonic stem cells, where it is marked by the H3K4me1 histone modification. 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 K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 13:Ctcf, distal CTCF/candidate insulator without open chromatin), with weaker activity in HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 1:Tss, active promoter, TSS/CpG island region). [provided by RefSeq, Jan 2023]
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    Genomic context

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    See LOC112163605 in Genome Data Viewer
    Location:
    12q
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (52024687..52025624)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (51988257..51989194)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (52418569..52418863)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene activin A receptor type 1B Neighboring gene RNA, U6 small nuclear 574, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4477 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:52399414-52400100 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4478 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:52401473-52402158 Neighboring gene TAMALIN antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:52402769-52403422 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:52403423-52404076 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:52404077-52404730 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:52404731-52405383 Neighboring gene trafficking regulator and scaffold protein tamalin Neighboring gene uncharacterized LOC124902934 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4479 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:52419409-52420346 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4480 Neighboring gene nuclear receptor subfamily 4 group A member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4481 Neighboring gene uncharacterized LOC107984510 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4482 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:52445362-52445919 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6389 Neighboring gene NR4A1 antisense RNA

    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. 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
    2. 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

    • Sharpr-MPRA regulatory region 2055

    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_056586.2 

      Range
      101..1038
      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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      52024687..52025624
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      51988257..51989194
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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