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LOC116276483 CRISPRi-validated cis-regulatory element chr17.5742 [ Homo sapiens (human) ]

Gene ID: 116276483, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116276483
Gene description
CRISPRi-validated cis-regulatory element chr17.5742
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 RNF213 (ring finger protein 213) gene on chromosome 17 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:
17q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (80257264..80257484)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (81157649..81157857)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (78231063..78231283)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene caspase recruitment domain family member 14 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:78178385-78179584 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:78183891-78184046 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12929 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9102 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9103 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78195951-78196788 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78196789-78197626 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78200105-78200606 Neighboring gene N-sulfoglucosamine sulfohydrolase Neighboring gene solute carrier family 26 member 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78209849-78210638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78210639-78211426 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78227308-78228024 Neighboring gene SLC26A11-RNF213 intergenic CAGE-defined mid-level expression enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9104 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9105 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9106 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78237270-78237826 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12934 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9107 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78247837-78248435 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78251821-78252439 Neighboring gene ring finger protein 213 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78258533-78259093 Neighboring gene RNF213 antisense RNA 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:78345568-78346767 Neighboring gene MPRA-validated peak3024 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78354122-78354622 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:78359110-78360309 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78369069-78369570 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78371216-78371723 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78371724-78372230 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12935 Neighboring gene microRNA 4730 Neighboring gene endonuclease V

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_067034.1 

    Range
    101..321
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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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    80257264..80257484
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    81157649..81157857
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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