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LOC115801422 CRISPRi-validated cis-regulatory element chr1.4289 [ Homo sapiens (human) ]

Gene ID: 115801422, updated on 10-Oct-2023

Summary

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Gene symbol
LOC115801422
Gene description
CRISPRi-validated cis-regulatory element chr1.4289
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 LAPTM5 (lysosomal protein transmembrane 5) 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 (30777481..30778146)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (30629784..30630449)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (31250328..31250993)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:31212057-31212616 Neighboring gene lysosomal protein transmembrane 5 Neighboring gene uncharacterized LOC105378620 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 618 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 619 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 620 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 621 Neighboring gene microRNA 4420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 622 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 623 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 624 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 625 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:31223351-31223894 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:31223895-31224436 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 628 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 629 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:31229428-31230224 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 630 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 631 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 632 Neighboring gene Sharpr-MPRA regulatory region 12480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:31246183-31246683 Neighboring gene uncharacterized LOC105378621 Neighboring gene CRISPRi-validated cis-regulatory element chr1.4291 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:31260718-31261230 Neighboring gene Sharpr-MPRA regulatory region 4114 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:31277163-31277830 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:31277831-31278496 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:31282779-31283279 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:31291425-31291931 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:31296724-31297226 Neighboring gene long intergenic non-protein coding RNA 1778 Neighboring gene RN7SK pseudogene 91

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_066080.1 

    Range
    101..766
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    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
    30777481..30778146
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    30629784..30630449
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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