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LOC115945202 CRISPRi-validated cis-regulatory element chr2.5899 [ Homo sapiens (human) ]

Gene ID: 115945202, updated on 10-Oct-2023

Summary

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Gene symbol
LOC115945202
Gene description
CRISPRi-validated cis-regulatory element chr2.5899
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 HIBCH (3-hydroxyisobutyryl-CoA hydrolase) gene on chromosome 2 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:
2q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (190781664..190782027)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (191270921..191271284)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (191646390..191646753)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12184 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12183 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16863 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16864 Neighboring gene NGFI-A binding protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16865 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16866 Neighboring gene uncharacterized LOC124907946 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:191624535-191625734 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:191655893-191657092 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:191708051-191709250 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12185 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:191734008-191734548 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:191734549-191735087 Neighboring gene uncharacterized LOC124906110 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16867 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12186 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12187 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12188 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12189 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:191746471-191747670 Neighboring gene glutaminase Neighboring gene signal transducer and activator of transcription 1 Neighboring gene RAB1A pseudogene 1

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_066574.1 

    Range
    101..464
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    190781664..190782027
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    191270921..191271284
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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