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LOC116216127 CRISPRi-validated cis-regulatory element chr11.592 [ Homo sapiens (human) ]

Gene ID: 116216127, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116216127
Gene description
CRISPRi-validated cis-regulatory element chr11.592
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 CHRNA10 (cholinergic receptor nicotinic alpha 10 subunit) gene on chromosome 11 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 LOC116216127 in Genome Data Viewer
Location:
11p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (2867156..2868924)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (2956378..2958146)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (2888386..2890154)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene potassium voltage-gated channel subfamily Q member 1 Neighboring gene uncharacterized LOC124902614 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:2818029-2818530 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:2821032-2821969 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:2826269-2826768 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:2832501-2833263 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:2833264-2834027 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:2848795-2849695 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:2856199-2857066 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:2857067-2857933 Neighboring gene KCNQ1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:2878979-2879960 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:2884189-2884886 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:2890154-2890662 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:2904223-2904722 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:2905995-2906830 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:2906831-2907666 Neighboring gene KCNQ1 downstream neighbor Neighboring gene cyclin dependent kinase inhibitor 1C

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_066892.1 

    Range
    101..1869
    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    2867156..2868924
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187585.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    99328..101095
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    2956378..2958146
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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