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    LOC116183041 CRISPRi-validated cis-regulatory element chr6.1165 [ Homo sapiens (human) ]

    Gene ID: 116183041, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC116183041
    Gene description
    CRISPRi-validated cis-regulatory element chr6.1165
    Gene type
    biological region
    Feature type(s)
    regulatory: 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. It was validated as a high-confidence cis-regulatory element for both the H2BC5 (H2B clustered histone 5) and H2B clustered histone 5 (H4 clustered histone 8) genes on chromosome 6 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Oct 2019]
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    Genomic context

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    Location:
    6p
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (26478142..26478577)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (26346547..26346982)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (26478370..26478805)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene butyrophilin subfamily 3 member A3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24242 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24243 Neighboring gene butyrophilin subfamily 2 member A1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:26465895-26467094 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24244 Neighboring gene uncharacterized LOC285819 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:26477169-26478368 Neighboring gene butyrophilin subfamily 1 member A1 pseudogene 1 Neighboring gene uncharacterized LOC107986583 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24245 Neighboring gene butyrophilin subfamily 1 member A1 Neighboring gene RNA, U6 small nuclear 502, pseudogene

    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

    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)

    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_066771.1 

      Range
      101..536
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      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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      26478142..26478577
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      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_025791780.1 Reference GRCh38.p14 PATCHES

      Range
      24322..24757
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      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      26346547..26346982
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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