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LOC115947637 CRISPRi-validated cis-regulatory element chr2.7218 [ Homo sapiens (human) ]

Gene ID: 115947637, updated on 10-Oct-2023

Summary

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Gene symbol
LOC115947637
Gene description
CRISPRi-validated cis-regulatory element chr2.7218
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 cis-regulatory element for the UBE2F (ubiquitin conjugating enzyme E2 F (putative)) 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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See LOC115947637 in Genome Data Viewer
Location:
2q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (237964148..237964551)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (238454150..238454553)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (238872790..238873193)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373960 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12482 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_57230 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:238850021-238850520 Neighboring gene uncharacterized LOC124908001 Neighboring gene CRISPRi-validated cis-regulatory element chr2.7219 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12483 Neighboring gene UBE2F-SCLY readthrough (NMD candidate) Neighboring gene ubiquitin conjugating enzyme E2 F (putative) Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:238936739-238937352 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:238941390-238941585 Neighboring gene RNA, U6 small nuclear 1333, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:238948423-238948923 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:238951349-238951541 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_57261 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12484 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12485 Neighboring gene selenocysteine lyase Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_57269 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:239002815-239003484 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:239003485-239004152 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:239004821-239005488 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:239005489-239006157 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:239006158-239006825 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:239006826-239007494

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_066580.1 

    Range
    101..504
    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
    237964148..237964551
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    238454150..238454553
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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