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LOC116158503 CRISPRi-validated cis-regulatory element chr4.2006 [ Homo sapiens (human) ]

Gene ID: 116158503, updated on 12-Sep-2024

Summary

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Gene symbol
LOC116158503
Gene description
CRISPRi-validated cis-regulatory element chr4.2006
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 ANTXR2 (ANTXR cell adhesion molecule 2) 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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See LOC116158503 in Genome Data Viewer
Location:
4q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (80179526..80180174)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (83509893..83510541)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (81100680..81101328)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900724 Neighboring gene CRISPRi-validated cis-regulatory element chr4.2002 Neighboring gene CRISPRi-validated cis-regulatory element chr4.2004 Neighboring gene ribosomal protein SA pseudogene 39 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15517 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15518 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15519 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15520 Neighboring gene Sharpr-MPRA regulatory region 11700 Neighboring gene PRDM8 antisense RNA 1 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr4:81111011-81111527 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr4:81111528-81112043 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr4:81117267-81117884 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:81117885-81118500 Neighboring gene PR/SET domain 8 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:81121978-81123177 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15521 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15522 Neighboring gene uncharacterized LOC124900725

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_066645.1 

    Range
    101..749
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    80179526..80180174
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    83509893..83510541
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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