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LOC116276460 CRISPRi-validated cis-regulatory element chr17.2188 [ Homo sapiens (human) ]

Gene ID: 116276460, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116276460
Gene description
CRISPRi-validated cis-regulatory element chr17.2188
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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. A subregion was validated as a cis-regulatory element for the PGAP3 (post-GPI attachment to proteins phospholipase 3) gene on chromosome 17 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. Another subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in primed human embryonic stem cells, where it is marked by the H3K27ac histone modification. [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC116276460 in Genome Data Viewer
Location:
17q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (38867437..38868311)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (39730487..39731361)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (37023690..37024303)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ribosomal protein S20 pseudogene 35 Neighboring gene tRNA-Cys (anticodon GCA) 14-1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12081 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:37024565-37025165 Neighboring gene tRNA-Cys (anticodon GCA) 2-2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12083 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8444 Neighboring gene tRNA-Cys (anticodon GCA) 4-1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:37027573-37028174 Neighboring gene LIM and SH3 protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8445 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:37036179-37036761 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:37037929-37038511 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:37049153-37049726 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:37051813-37052334 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:37052335-37052856 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:37052857-37053378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12084 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:37054945-37055466 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:37055467-37055986 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:37057617-37058242 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:37068165-37069124 Neighboring gene microRNA 6779

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. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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)

General gene information

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Other Names

  • H3K27ac hESC enhancer GRCh37_chr17:37023962-37024564

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_067011.2 

    Range
    101..975
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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
    38867437..38868311
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    39730487..39731361
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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