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LOC116268459 CRISPRi-validated cis-regulatory element chr14.1538 [ Homo sapiens (human) ]

Gene ID: 116268459, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116268459
Gene description
CRISPRi-validated cis-regulatory element chr14.1538
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 cis-regulatory element for the NEK9 (NIMA related kinase 9) gene on chromosome 14 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 LOC116268459 in Genome Data Viewer
Location:
14q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (75229743..75230298)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (69439122..69439677)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (75696446..75697001)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene transmembrane p24 trafficking protein 10 Neighboring gene Sharpr-MPRA regulatory regions 714 and 744 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:75619067-75619731 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:75643139-75643711 Neighboring gene RNA, U4atac small nuclear 14, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:75687528-75688425 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:75688426-75689322 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:75689323-75690220 Neighboring gene VISTA enhancer hs1657 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8739 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8740 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr14:75720649-75721848 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:75723647-75724146 Neighboring gene VISTA enhancer hs1481 Neighboring gene uncharacterized LOC124903434 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5941 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5942 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5943 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:75745521-75746448 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:75746449-75747374 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:75747401-75747960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:75747961-75748520 Neighboring gene Fos proto-oncogene, AP-1 transcription factor subunit

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_066974.1 

    Range
    101..656
    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    75229743..75230298
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    69439122..69439677
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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