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LOC116268452 CRISPRi-validated cis-regulatory element chr12.4732 [ Homo sapiens (human) ]

Gene ID: 116268452, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116268452
Gene description
CRISPRi-validated cis-regulatory element chr12.4732
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 SCARB1 (scavenger receptor class B member 1) gene on chromosome 12 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. The SCARB1 regulatory target for this locus is involved in SARS-CoV-2 infection. [provided by RefSeq, Dec 2022]
Annotation information
Note: This locus has been reviewed for its involvement in coronavirus biology, and is involved in host gene regulation.
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Genomic context

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Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (124887120..124887569)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (124892248..124892697)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (125371666..125372115)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:125270855-125271355 Neighboring gene uncharacterized LOC124903046 Neighboring gene scavenger receptor class B member 1 Neighboring gene MPRA-validated peak2031 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:125282050-125282560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:125282561-125283071 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_25196 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:125301275-125301774 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:125309151-125309872 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:125309873-125310594 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7304 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:125323854-125324380 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:125324381-125324905 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7305 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:125346238-125346764 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5067 Neighboring gene uncharacterized LOC105370050 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7306 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_25236 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:125351043-125352242 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:125369125-125369812 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7308 Neighboring gene RNA, U6 small nuclear 927, pseudogene Neighboring gene Sharpr-MPRA regulatory region 9680 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:125398493-125399450 Neighboring gene ubiquitin C

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_066967.1 

    Range
    101..550
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    124887120..124887569
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    124892248..124892697
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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