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LOC116216119 CRISPRi-validated cis-regulatory element chr10.3525 [ Homo sapiens (human) ]

Gene ID: 116216119, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116216119
Gene description
CRISPRi-validated cis-regulatory element chr10.3525
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 LCOR (ligand dependent nuclear receptor corepressor) gene on chromosome 10 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 LOC116216119 in Genome Data Viewer
Location:
10q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (96830646..96830845)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (97711559..97711758)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (98590403..98590602)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2660 Neighboring gene ribosomal protein L13a pseudogene 5 Neighboring gene uncharacterized LOC102723665 Neighboring gene H3K27ac hESC enhancers GRCh37_chr10:98591864-98592578 and GRCh37_chr10:98592579-98593294 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:98593295-98594008 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98597029-98597529 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98599567-98600066 Neighboring gene Sharpr-MPRA regulatory region 4280 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98602601-98603100 Neighboring gene microRNA 607 Neighboring gene ligand dependent nuclear receptor corepressor Neighboring gene high mobility group nucleosomal binding domain 2 pseudogene 35 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:98744001-98744502 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:98744503-98745002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98761702-98762390 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98780664-98781497 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98790940-98791510 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98791511-98792081 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:98794025-98794781 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98797839-98798339 Neighboring gene slit guidance ligand 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2666 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:98829552-98830751 Neighboring gene Sharpr-MPRA regulatory region 3512 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:98839846-98840622 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98850461-98851078 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98860158-98861022 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98861023-98861885 Neighboring gene SLIT1 antisense RNA 1

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_066886.1 

    Range
    101..300
    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    96830646..96830845
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    97711559..97711758
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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