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LOC116309126 CRISPRi-validated cis-regulatory element chr22.250 [ Homo sapiens (human) ]

Gene ID: 116309126, updated on 12-Sep-2024

Summary

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Gene symbol
LOC116309126
Gene description
CRISPRi-validated cis-regulatory element chr22.250
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 DGCR2 (DiGeorge syndrome critical region gene 2) gene on chromosome 22 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:
22q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (19627502..19627582)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (20004349..20004429)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (19615025..19615105)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19509616-19510548 Neighboring gene claudin 5 Neighboring gene MPRA-validated peak4453 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19531837-19532336 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19542168-19542870 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19542871-19543573 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:19554961-19555296 Neighboring gene long intergenic non-protein coding RNA 895 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19583904-19584446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19585482-19585982 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19585983-19586483 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19592881-19593448 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19593449-19594016 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19594499-19595072 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19604675-19605254 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19605255-19605833 Neighboring gene Sharpr-MPRA regulatory region 15144 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19607854-19608615 Neighboring gene chromosome 3 open reading frame 38 pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr22:19640940-19641163 Neighboring gene uncharacterized LOC100420103

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_067095.1 

    Range
    101..181
    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    19627502..19627582
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    20004349..20004429
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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