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LOC116268427 CRISPRi-validated cis-regulatory element chr12.283 [ Homo sapiens (human) ]

Gene ID: 116268427, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116268427
Gene description
CRISPRi-validated cis-regulatory element chr12.283
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 CD9 (CD9 molecule) gene on chromosome 12 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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Location:
12p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (6263832..6264518)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (6271448..6272134)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (6372998..6373684)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369623 Neighboring gene uncharacterized LOC105369622 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6289294-6289864 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5842 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6299563-6300248 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6300249-6300934 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4157 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6308438-6309050 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6309051-6309662 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6310889-6311501 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6311502-6312113 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6319522-6320145 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6320176-6320677 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6323515-6324018 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr12:6324019-6324520 and GRCh37_chr12:6324521-6325024 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:6327115-6328314 Neighboring gene Sharpr-MPRA regulatory region 3368 Neighboring gene CD9 molecule Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6332057-6332610 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6332611-6333162 Neighboring gene uncharacterized LOC105369625 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6333163-6333716 Neighboring gene Sharpr-MPRA regulatory region 10655 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6350388-6350888 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6350889-6351389 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6378001-6378746 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4158 Neighboring gene ATP synthase membrane subunit f pseudogene 5 Neighboring gene Sharpr-MPRA regulatory region 10601 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6390295-6390794 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:6402555-6402765 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:6404819-6405319 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6418662-6419382 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4159 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5844 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6427837-6428456 Neighboring gene pleckstrin homology and RhoGEF domain containing G6 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6432098-6432639 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5846 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6433181-6433722 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6433723-6434262

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_066942.1 

    Range
    101..787
    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
    6263832..6264518
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    6271448..6272134
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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