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LOC116183096 CRISPRi-validated cis-regulatory element chr7.3907 [ Homo sapiens (human) ]

Gene ID: 116183096, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116183096
Gene description
CRISPRi-validated cis-regulatory element chr7.3907
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 RELN (reelin) gene on chromosome 7 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Oct 2019]
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Genomic context

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See LOC116183096 in Genome Data Viewer
Location:
7q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (103995975..103996570)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (105310003..105310598)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (103636422..103637017)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene SLC26A5 antisense RNA 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:103130126-103131325 Neighboring gene uncharacterized LOC105375435 Neighboring gene Sharpr-MPRA regulatory region 15155 Neighboring gene RN7SK pseudogene 86 Neighboring gene reelin Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:103301048-103302247 Neighboring gene Sharpr-MPRA regulatory region 11588 Neighboring gene MPRA-validated peak6667 silencer Neighboring gene Sharpr-MPRA regulatory region 1232 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:103691916-103692125 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:103765716-103765879 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26444 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26445 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:103904410-103905609 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:103916337-103917536 Neighboring gene origin recognition complex subunit 5 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:104001319-104001836 Neighboring gene LHFPL tetraspan subfamily member 3 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:104169841-104171040 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:104190573-104191772 Neighboring gene eukaryotic translation initiation factor 4B pseudogene 6

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. The DNA sequence of human chromosome 7. Hillier LW, et al. Nature, 2003 Jul 10. PMID 12853948
  2. 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
  3. An integrated encyclopedia of DNA elements in the human genome. ENCODE Project Consortium. Nature, 2012 Sep 6. PMID 22955616, Free PMC Article
  4. 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_066824.1 

    Range
    101..696
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    103995975..103996570
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    105310003..105310598
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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