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    LOC115801441 CRISPRi-validated cis-regulatory element chr1.8052 [ Homo sapiens (human) ]

    Gene ID: 115801441, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC115801441
    Gene description
    CRISPRi-validated cis-regulatory element chr1.8052
    Gene type
    biological region
    Feature type(s)
    regulatory: enhancer, transcriptional_cis_regulatory_region
    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 represents a DNase I hypersensitive site (DHS) that was predicted to be an enhancer by the ENCODE (ENCyclopedia Of DNA Elements) project based on various combinations of H3K27 acetylation and binding of p300, GATA1 and RNA polymerase II in K562 erythroleukemia cells. A subregion was validated as a high-confidence cis-regulatory element for the IGSF3 (immunoglobulin superfamily member 3) gene on chromosome 1, and also at lower confidence for the TTF2 (transcription termination factor 2) gene, based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. Another subregion 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 H3K27ac and H3K4me1 histone modifications. [provided by RefSeq, Jan 2023]
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    Genomic context

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    Location:
    1p
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (116687162..116688778)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (116697623..116699231)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (117229784..117230655)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene immunoglobulin superfamily member 3 Neighboring gene uncharacterized LOC105378924 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1234 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:117142207-117142708 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:117150835-117151334 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:117156699-117157269 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:117161725-117162232 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:117184821-117185506 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:117185507-117186190 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:117188080-117188811 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:117188812-117189542 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:117189543-117190273 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1235 Neighboring gene microRNA 320b-1 Neighboring gene long intergenic non-protein coding RNA 2868 Neighboring gene uncharacterized LOC105378926 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene 64

    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. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. Gasperini M, et al. Cell, 2019 Jan 10. PMID 30612741, Free PMC Article
    2. An integrated encyclopedia of DNA elements in the human genome. ENCODE Project Consortium. Nature, 2012 Sep 6. PMID 22955616, Free PMC Article
    3. The accessible chromatin landscape of the human genome. Thurman RE, et al. Nature, 2012 Sep 6. PMID 22955617, Free PMC Article
    4. 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_chr1:117230448-117231400

    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_066099.2 

      Range
      101..1717
      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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      116687162..116688778
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      116697623..116699231
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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