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LOC115801449 CRISPRi-validated cis-regulatory element chr1.9249 [ Homo sapiens (human) ]

Gene ID: 115801449, updated on 10-Oct-2023

Summary

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Gene symbol
LOC115801449
Gene description
CRISPRi-validated cis-regulatory element chr1.9249
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 METTL25B (methyltransferase like 25B, formerly known as RRNAD1) gene on chromosome 1 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Mar 2023]
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Genomic context

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See LOC115801449 in Genome Data Viewer
Location:
1q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (157274686..157275184)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (156411592..156412090)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (157244476..157244974)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr1:157107959-157108294 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:157108646-157109251 Neighboring gene Sharpr-MPRA regulatory region 11922 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:157127246-157127757 Neighboring gene CYCS pseudogene 52 Neighboring gene Sharpr-MPRA regulatory region 527 Neighboring gene ETS variant transcription factor 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:157142571-157143072 Neighboring gene uncharacterized LOC107985211 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1887 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:157163574-157163806 Neighboring gene uncharacterized LOC105371456 Neighboring gene NANOG hESC enhancer GRCh37_chr1:157243171-157243713 Neighboring gene SLAM family member 5 Neighboring gene long intergenic non-protein coding RNA 2772 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:157279563-157280762 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1446 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1888 Neighboring gene NANOG hESC enhancer GRCh37_chr1:157391313-157391814 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1889 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1890 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:157489840-157491039 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1891 Neighboring gene Fc receptor like 5

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_066107.1 

    Range
    101..599
    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
    157274686..157275184
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    156411592..156412090
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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