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LOC115945187 CRISPRi-validated cis-regulatory element chr2.4367 [ Homo sapiens (human) ]

Gene ID: 115945187, updated on 10-Oct-2023

Summary

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Gene symbol
LOC115945187
Gene description
CRISPRi-validated cis-regulatory element chr2.4367
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 RALB (RAS like proto-oncogene B) 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 (120343288..120343778)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (120778028..120778518)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (121100864..121101354)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373583 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121000550-121001500 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121003065-121003640 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121003641-121004217 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11918 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16459 Neighboring gene RAS like proto-oncogene B Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:121041209-121041722 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16460 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:121048087-121048782 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121070991-121071514 Neighboring gene uncharacterized LOC105373584 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121082735-121083235 Neighboring gene putative cuticle collagen 91 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121110159-121110862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121110863-121111564 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121114094-121114669 Neighboring gene inhibin subunit beta B Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:121130783-121131676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121133461-121134352 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121152410-121153223 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121187849-121188837 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121199691-121200316 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:121209011-121209167 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:121210803-121212002 Neighboring gene NANOG hESC enhancer GRCh37_chr2:121214333-121214894 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:121223679-121224221 Neighboring gene long intergenic non-protein coding RNA 1101

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_066568.1 

    Range
    101..591
    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
    120343288..120343778
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    120778028..120778518
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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