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LOC116158498 CRISPRi-validated cis-regulatory element chr4.1974 [ Homo sapiens (human) ]

Gene ID: 116158498, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116158498
Gene description
CRISPRi-validated cis-regulatory element chr4.1974
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 BMP2K (BMP2 inducible kinase) gene on chromosome 4 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:
4q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (78691839..78692517)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (82027431..82028109)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (79612993..79613671)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U13 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:79566785-79567984 Neighboring gene long intergenic non-protein coding RNA 1094 Neighboring gene HIG1 hypoxia inducible domain family member 1A pseudogene 13 Neighboring gene CRISPRi-validated cis-regulatory element chr4.1973 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:79627314-79627946 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr4:79635971-79636917 Neighboring gene uncharacterized LOC101928893 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:79639668-79640239 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:79640240-79640810 Neighboring gene Sharpr-MPRA regulatory region 1360 Neighboring gene CRISPRi-validated cis-regulatory element chr4.1978 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:79643097-79643668 Neighboring gene CRISPRi-validated cis-regulatory element chr4.1979 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15511 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21649 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21650 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21651 Neighboring gene ribosomal protein S21 pseudogene 3

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_066640.1 

    Range
    101..779
    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    78691839..78692517
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    82027431..82028109
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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