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LOC116216126 CRISPRi-validated cis-regulatory element chr11.30 [ Homo sapiens (human) ]

Gene ID: 116216126, updated on 27-Aug-2024

Summary

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Gene symbol
LOC116216126
Gene description
CRISPRi-validated cis-regulatory element chr11.30
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 IFITM1 (interferon induced transmembrane protein 1) gene on chromosome 11 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. The IFITM1 regulatory target for this locus is relevant for coronavirus biology given its role in restricting cellular entry by diverse viral pathogens, including SARS-CoV-2. [provided by RefSeq, Dec 2022]
Annotation information
Note: This locus has been reviewed for its involvement in coronavirus biology, and is involved in host gene regulation.
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Genomic context

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Location:
11p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (350815..351291)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (391682..392158)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (350815..351291)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:313981-314536 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4264 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4265 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2994 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2995 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2996 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4266 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:316761-317316 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4267 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:318431-318986 Neighboring gene uncharacterized LOC105376505 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:318987-319542 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:320655-321210 Neighboring gene interferon induced transmembrane protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4268 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4269 Neighboring gene interferon induced transmembrane protein 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4270 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4271 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:333329-333882 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:333883-334436 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4272 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:353490-353656 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:354319-354895 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:355877-356829 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:368032-368570 Neighboring gene beta-1,4-N-acetyl-galactosaminyltransferase 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:380111-380268 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:393662-394424 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:396383-396912 Neighboring gene plakophilin 3

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_066891.1 

    Range
    101..577
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    350815..351291
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    391682..392158
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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