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LOC116276476 CRISPRi-validated cis-regulatory element chr17.4314 [ Homo sapiens (human) ]

Gene ID: 116276476, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116276476
Gene description
CRISPRi-validated cis-regulatory element chr17.4314
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 ICAM2 (intercellular adhesion molecule 2) gene on chromosome 17 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:
17q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (64024166..64024603)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (64894911..64895348)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (62101526..62101963)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8836 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:62075897-62076874 Neighboring gene PRR29 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:62083286-62083980 Neighboring gene proline rich 29 Neighboring gene intercellular adhesion molecule 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12571 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:62097827-62098327 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12573 Neighboring gene CRISPRi-validated cis-regulatory element chr17.4315 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:62132617-62133360 Neighboring gene endoplasmic reticulum to nucleus signaling 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:62133361-62134104 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8837 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12576 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12577 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8838 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12578 Neighboring gene Sharpr-MPRA regulatory region 10488 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12579 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12580 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12581 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12582 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8839 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8840 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12583 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12584 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12585 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12586 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:62223017-62223571 Neighboring gene small nucleolar RNA, C/D box 104 Neighboring gene small nucleolar RNA host gene 25

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_067027.1 

    Range
    101..538
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    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    64024166..64024603
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    64894911..64895348
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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