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LOC115804237 CRISPRi-validated cis-regulatory element chr1.10450 [ Homo sapiens (human) ]

Gene ID: 115804237, updated on 12-Sep-2024

Summary

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Gene symbol
LOC115804237
Gene description
CRISPRi-validated cis-regulatory element chr1.10450
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 PTPRC (protein tyrosine phosphatase receptor type C) gene on chromosome 1 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Sep 2019]
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Genomic context

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See LOC115804237 in Genome Data Viewer
Location:
1q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (198633686..198634101)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (197893610..197894025)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (198602816..198603231)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATPase H+ transporting V1 subunit G3 Neighboring gene uncharacterized LOC124904478 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:198637893-198639092 Neighboring gene protein tyrosine phosphatase receptor type C Neighboring gene PTPRC intron CAGE-defined mid-level expression enhancer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:198670715-198671264 Neighboring gene phosphatidylethanolamine binding protein 1 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1667 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:198776880-198778079 Neighboring gene MIR181A1 host gene Neighboring gene microRNA 181b-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_066119.1 

    Range
    101..516
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    198633686..198634101
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NW_003315907.2 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    275091..275506
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    197893610..197894025
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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