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LOC116216118 CRISPRi-validated cis-regulatory element chr10.3436 [ Homo sapiens (human) ]

Gene ID: 116216118, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116216118
Gene description
CRISPRi-validated cis-regulatory element chr10.3436
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 PDLIM1 (PDZ and LIM domain 1) 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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Location:
10q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (95297343..95297926)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (96176522..96177105)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (97057100..97057683)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984257 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:96961907-96962201 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:96987152-96987893 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:96988638-96989207 Neighboring gene Sharpr-MPRA regulatory region 8644 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr10:96990347-96990915 and GRCh37_chr10:96990916-96991485 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:97000971-97001634 Neighboring gene acyl-CoA synthetase medium chain family member 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:97001635-97002298 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3792 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3793 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:97020155-97020844 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:97024067-97024842 Neighboring gene PDZ and LIM domain 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3794 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2640 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2641 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2642 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2643 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2644 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3795 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3797 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3798 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:97054719-97055315 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3799 Neighboring gene Sharpr-MPRA regulatory region 12220 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:97106670-97107322 Neighboring gene sorbin and SH3 domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2645 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2646 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3800 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:97190228-97190728 Neighboring gene Sharpr-MPRA regulatory region 10569 Neighboring gene VISTA enhancer hs2353 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:97291131-97291878 Neighboring gene NANOG hESC enhancer GRCh37_chr10:97299485-97299986 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:97311480-97312414 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:97320711-97321473 Neighboring gene Sharpr-MPRA regulatory region 13709 Neighboring gene RPS3A pseudogene 36

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_066885.1 

    Range
    101..684
    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
    95297343..95297926
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    96176522..96177105
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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