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LOC115801438 CRISPRi-validated cis-regulatory element chr1.7635 [ Homo sapiens (human) ]

Gene ID: 115801438, updated on 10-Oct-2023

Summary

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Gene symbol
LOC115801438
Gene description
CRISPRi-validated cis-regulatory element chr1.7635
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 SARS1 (seryl-tRNA synthetase 1) 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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Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (109889137..109889561)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (109899274..109899698)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (110431759..110432183)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904258 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:110303188-110303917 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:110312201-110313156 Neighboring gene Sharpr-MPRA regulatory region 10752 Neighboring gene EPS8 signaling adaptor L3 Neighboring gene Sharpr-MPRA regulatory region 9477 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:110329469-110330352 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:110330353-110331236 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1452 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:110350451-110351094 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:110351095-110351737 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1453 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1454 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1159 Neighboring gene NADH:ubiquinone oxidoreductase subunit A5 pseudogene 10 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1160 Neighboring gene long intergenic non-protein coding RNA 1768 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:110407495-110408040 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:110420113-110420301 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:110422869-110423369 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:110423473-110424313 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:110424314-110425153 Neighboring gene Sharpr-MPRA regulatory region 12342 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1455 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1456 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:110453680-110454180 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:110454181-110454681 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1457 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:110473698-110474646 Neighboring gene colony stimulating factor 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:110502441-110503012 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:110503013-110503582 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1163 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1164 Neighboring gene adenosylhomocysteinase like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1458 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:110560640-110561839

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_066096.1 

    Range
    101..525
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    109889137..109889561
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    109899274..109899698
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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