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LOC116186934 CRISPRi-validated cis-regulatory element chr8.2347 [ Homo sapiens (human) ]

Gene ID: 116186934, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116186934
Gene description
CRISPRi-validated cis-regulatory element chr8.2347
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 the INTS8 (integrator complex subunit 8) gene on chromosome 8 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Nov 2019]
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Genomic context

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Location:
8q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (95160142..95160346)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (96285389..96285593)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (96172370..96172574)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene NADH:ubiquinone oxidoreductase complex assembly factor 6 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19379 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27640 Neighboring gene MIR3150B host gene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27641 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27642 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27643 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27644 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27645 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19380 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27646 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27647 Neighboring gene microRNA 3150b Neighboring gene microRNA 3150a Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19381 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19382 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27648 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19383 Neighboring gene uncharacterized LOC124901982 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19384 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27649 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27650 Neighboring gene pleckstrin homology and FYVE domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27651 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27652 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27653 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27654 Neighboring gene long intergenic non-protein coding RNA 1298 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27655 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:96281415-96282054 Neighboring gene CFAP418 antisense RNA 1 Neighboring gene cilia and flagella associated protein 418

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. Toward a complete human genome sequence. Sanger Center, et al. Genome Res, 1998 Nov. PMID 9847074

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_066854.1 

    Range
    101..305
    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    95160142..95160346
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    96285389..96285593
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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