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LOC115801437 CRISPRi-validated cis-regulatory element chr1.7484 [ Homo sapiens (human) ]

Gene ID: 115801437, updated on 12-Sep-2024

Summary

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Gene symbol
LOC115801437
Gene description
CRISPRi-validated cis-regulatory element chr1.7484
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 EEIG2 (EEIG family member 2, formerly known as FAM102B) 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 LOC115801437 in Genome Data Viewer
Location:
1p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (108533625..108534200)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (108566607..108567183)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (109076247..109076822)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:109045678-109046211 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1134 Neighboring gene ST13, Hsp70 interacting protein pseudogene 21 Neighboring gene RPL7L1 pseudogene 21 Neighboring gene NANOG hESC enhancer GRCh37_chr1:109060171-109060846 Neighboring gene Sharpr-MPRA regulatory region 3357 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1135 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1423 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1424 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:109111447-109111662 Neighboring gene EEIG family member 2 Neighboring gene MPRA-validated peak351 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:109203434-109204023 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:109204024-109204612 Neighboring gene HEN methyltransferase 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_066095.1 

    Range
    101..676
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    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
    108533625..108534200
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_017852928.1 Reference GRCh38.p14 PATCHES

    Range
    545221..545796
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    108566607..108567183
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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