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LOC115945159 CRISPRi-validated cis-regulatory element chr2.2452 [ Homo sapiens (human) ]

Gene ID: 115945159, updated on 10-Oct-2023

Summary

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Gene symbol
LOC115945159
Gene description
CRISPRi-validated cis-regulatory element chr2.2452
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 CNRIP1 (cannabinoid receptor interacting protein 1) gene on chromosome 2 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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Location:
2p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (68352631..68353045)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (68363201..68363615)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (68579763..68580177)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985892 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11589 Neighboring gene cannabinoid receptor interacting protein 1 Neighboring gene Sharpr-MPRA regulatory region 10638 Neighboring gene uncharacterized LOC102724389 Neighboring gene uncharacterized LOC101927723 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15948 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15949 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15950 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15951 Neighboring gene pleckstrin Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15952 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11590 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11591 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15953 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15954 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15955 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15956 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11592 Neighboring gene WDR4 pseudogene 2

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_066559.1 

    Range
    101..515
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    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    68352631..68353045
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    68363201..68363615
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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