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LOC116309123 CRISPRi-validated cis-regulatory element chr21.79 [ Homo sapiens (human) ]

Gene ID: 116309123, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116309123
Gene description
CRISPRi-validated cis-regulatory element chr21.79
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 NRIP1 (nuclear receptor interacting protein 1) gene on chromosome 21 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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See LOC116309123 in Genome Data Viewer
Location:
21q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (15210285..15210677)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (13565755..13566147)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (16582605..16582997)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985483 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:16493536-16494052 Neighboring gene Sharpr-MPRA regulatory region 10595 Neighboring gene Sharpr-MPRA regulatory region 10306 Neighboring gene uncharacterized LOC124905047 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr21:16594333-16594922 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr21:16614729-16615343 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr21:16614113-16614728 Neighboring gene uncharacterized LOC105369292 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:16662777-16663306 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr21:16665453-16666075 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:16698845-16699655 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr21:16738058-16739257 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr21:16739664-16740201 Neighboring gene uncharacterized LOC101927745 Neighboring gene uncharacterized LOC124905055

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_067092.1 

    Range
    101..493
    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    15210285..15210677
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    13565755..13566147
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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