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LOC115801425 CRISPRi-validated cis-regulatory element chr1.5052 [ Homo sapiens (human) ]

Gene ID: 115801425, updated on 10-Oct-2023

Summary

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Gene symbol
LOC115801425
Gene description
CRISPRi-validated cis-regulatory element chr1.5052
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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. A subregion was validated as a high-confidence cis-regulatory element for the MANEAL (mannosidase endo-alpha like) gene on chromosome 1 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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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 (38527394..38527650)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (38394615..38394871)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (38993066..38993269)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378657 Neighboring gene uncharacterized LOC107984943 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:38918219-38918720 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 793 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 794 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 795 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:38949916-38950676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:38950677-38951437 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:38955288-38956062 Neighboring gene long intergenic non-protein coding RNA 1685 Neighboring gene Sharpr-MPRA regulatory region 1530 Neighboring gene uncharacterized LOC105378658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:38995999-38996641 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:39021300-39022499 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 797 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:39025118-39025733 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:39034058-39034665 Neighboring gene MPRA-validated peak186 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:39065535-39066150 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:39066151-39066766 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:39073721-39074510 Neighboring gene uncharacterized LOC105378660 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:39165731-39165950 Neighboring gene VISTA enhancer hs1031 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:39206875-39207549 Neighboring gene Sharpr-MPRA regulatory region 12321 Neighboring gene NANOG hESC enhancer GRCh37_chr1:39212546-39213129 Neighboring gene HSPA5 pseudogene 1 Neighboring gene VISTA enhancer hs1139 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:39253877-39254442 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 798 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:39281537-39282038 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:39282039-39282538 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 688 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:39285036-39285203 Neighboring gene Sharpr-MPRA regulatory region 3933 Neighboring gene Ras related GTP binding C

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
  4. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 796

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_066083.2 

    Range
    101..357
    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
    38527394..38527650
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    38394615..38394871
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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