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LOC116216149 CRISPRi-validated cis-regulatory element chr11.3768 [ Homo sapiens (human) ]

Gene ID: 116216149, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116216149
Gene description
CRISPRi-validated cis-regulatory element chr11.3768
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 MYEOV (myeloma overexpressed) 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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Location:
11q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (69401490..69402125)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (69418639..69419274)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (69216258..69216893)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69078345-69078844 Neighboring gene interferon induced transmembrane protein 9 pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:69088091-69088958 Neighboring gene uncharacterized LOC105369370 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5158 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69153613-69154114 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69154115-69154614 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69157262-69158194 Neighboring gene MPRA-validated peak1324 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69214023-69214785 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69215486-69215986 Neighboring gene CRISPRi-validated cis-regulatory element chr11.3769 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:69234157-69234732 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:69235307-69235881 Neighboring gene long intergenic non-protein coding RNA 2953 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:69249331-69250160 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:69251823-69252654 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:69253485-69254316 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5159 Neighboring gene long intergenic non-protein coding RNA 2952 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3693 Neighboring gene uncharacterized LOC124902703

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_066914.1 

    Range
    101..736
    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
    69401490..69402125
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    69418639..69419274
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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