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LOC116216116 CRISPRi-validated cis-regulatory element chr10.2662 [ Homo sapiens (human) ]

Gene ID: 116216116, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116216116
Gene description
CRISPRi-validated cis-regulatory element chr10.2662
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 VCL (vinculin) gene on chromosome 10 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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See LOC116216116 in Genome Data Viewer
Location:
10q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (73993230..73993513)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (74864619..74864902)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (75752988..75753271)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902454 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:75648172-75649130 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:75668366-75669565 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2495 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:75672789-75673988 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:75679930-75680578 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:75680579-75681225 Neighboring gene chromosome 10 putative open reading frame 55 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr10:75691709-75692908 Neighboring gene plasminogen activator, urokinase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3584 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3585 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:75716666-75717173 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3586 Neighboring gene Sharpr-MPRA regulatory region 4338 Neighboring gene VISTA enhancer hs2142 Neighboring gene Sharpr-MPRA regulatory region 295 Neighboring gene CRISPRi-validated cis-regulatory element chr10.2661 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2498 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3587 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:75758175-75758826 Neighboring gene Sharpr-MPRA regulatory region 4496 Neighboring gene vinculin Neighboring gene uncharacterized LOC124902455 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3588 Neighboring gene uncharacterized LOC124902458

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_066883.1 

    Range
    101..384
    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    73993230..73993513
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    74864619..74864902
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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