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LOC116158527 CRISPRi-validated cis-regulatory element chr5.4451 [ Homo sapiens (human) ]

Gene ID: 116158527, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116158527
Gene description
CRISPRi-validated cis-regulatory element chr5.4451
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 both the DUSP1 (dual specificity phosphatase 1) and STC2 (stanniocalcin 2) genes on chromosome 5 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Oct 2019]
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Genomic context

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Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (172802257..172803165)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (173342365..173343273)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (172229260..172230168)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr5:172194940-172195132 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16625 Neighboring gene VISTA enhancer hs1828 Neighboring gene uncharacterized LOC105377730 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23645 Neighboring gene dual specificity phosphatase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:172214701-172215202 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:172232818-172233634 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:172233916-172235115 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:172246893-172247394 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:172250515-172251016 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:172251017-172251516 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16627 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16629 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:172262000-172262992 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16628 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:172262993-172263984 Neighboring gene uncharacterized LOC124901135 Neighboring gene endoplasmic reticulum-golgi intermediate compartment 1 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:172276540-172277739 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:172281789-172282290 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:172285332-172285509 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:172286171-172287171 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:172290019-172290520 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:172304495-172305470 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:172305471-172306446 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23647 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:172328739-172329249 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:172331587-172332786 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23648 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:172341803-172342303 Neighboring gene microRNA 10523

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
  4. Toward a complete human genome sequence. Sanger Center, et al. Genome Res, 1998 Nov. PMID 9847074

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_066669.1 

    Range
    101..1009
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    172802257..172803165
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    173342365..173343273
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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