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LOC116276489 CRISPRi-validated cis-regulatory element chr18.397 [ Homo sapiens (human) ]

Gene ID: 116276489, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116276489
Gene description
CRISPRi-validated cis-regulatory element chr18.397
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 IMPA2 (inositol monophosphatase 2) gene on chromosome 18 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. Two subregions were also shown to be active enhancers by ChIP-STARR-seq in naive human embryonic stem cells, where both are marked by the H3K27ac and H3K4me1 histone modifications and one is additionally associated with the NANOG transcription factor. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC116276489 in Genome Data Viewer
Location:
18p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (11947066..11948602)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (12109780..12111316)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (11947158..11947945)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene G protein subunit alpha L Neighboring gene uncharacterized LOC124904252 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9301 Neighboring gene uncharacterized LOC101927511 Neighboring gene metallophosphoesterase 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:11951641-11952330 Neighboring gene Sharpr-MPRA regulatory region 7933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13098 Neighboring gene inositol monophosphatase 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:12038197-12038698 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9304 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13099 Neighboring gene kinesin-like protein KIF1C Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:12058991-12059532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:12059533-12060072 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:12060615-12061154

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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, Free PMC Article
  5. 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

  • ATAC-STARR-seq lymphoblastoid active region 13097
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:11947834-11948601
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:11947065-11947833

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_067040.2 

    Range
    101..1637
    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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    11947066..11948602
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    12109780..12111316
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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