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LOC115945155 CRISPRi-validated cis-regulatory element chr2.1678 [ Homo sapiens (human) ]

Gene ID: 115945155, updated on 10-Oct-2023

Summary

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Gene symbol
LOC115945155
Gene description
CRISPRi-validated cis-regulatory element chr2.1678
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 THADA (THADA armadillo repeat containing) 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:
2p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (42989346..42989519)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (42994604..42994777)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (43216486..43216659)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374568 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43153519-43154204 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43154205-43154890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:43159155-43159942 Neighboring gene uncharacterized LOC112268413 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:43172691-43173490 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43216953-43217505 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15656 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:43227725-43228506 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:43253326-43254142 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:43254143-43254958 Neighboring gene long intergenic non-protein coding RNA 1819 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43268142-43269084 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43269085-43270026 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43270027-43270968 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:43273691-43274404 Neighboring gene uncharacterized LOC107985876 Neighboring gene uncharacterized LOC124907756 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:43307601-43308303 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43310546-43311312

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_066555.1 

    Range
    101..274
    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
    42989346..42989519
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    42994604..42994777
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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