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LOC116158543 CRISPRi-validated cis-regulatory element chr6.704 [ Homo sapiens (human) ]

Gene ID: 116158543, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116158543
Gene description
CRISPRi-validated cis-regulatory element chr6.704
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 cis-regulatory element for the RNF182 (ring finger protein 182) gene on chromosome 6 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 LOC116158543 in Genome Data Viewer
Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (13992618..13993055)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (13865061..13865498)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (13992849..13993286)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16939 Neighboring gene uncharacterized LOC107986571 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16940 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24040 Neighboring gene mitochondrial calcium uniporter regulator 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:13872467-13873049 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16941 Neighboring gene CRISPRi-validated cis-regulatory element chr6.697 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:13924078-13924578 Neighboring gene NANOG hESC enhancer GRCh37_chr6:13944174-13944689 Neighboring gene ring finger protein 182 Neighboring gene mitochondrial ribosomal protein L35 pseudogene 1 Neighboring gene CRISPRi-validated cis-regulatory element chr6.702 Neighboring gene CRISPRi-validated cis-regulatory element chr6.703 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:14001334-14002533 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:14035147-14036346 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:14069795-14069896 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24041 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24042 Neighboring gene NANOG hESC enhancer GRCh37_chr6:14088959-14089460 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24043 Neighboring gene CRISPRi-FlowFISH-validated CD83 regulatory element GRCh37_chr6:14095567-14096067 Neighboring gene uncharacterized LOC105374939 Neighboring gene CRISPRi-validated cis-regulatory element chr6.709 Neighboring gene uncharacterized LOC124901265

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_066684.1 

    Range
    101..538
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    13992618..13993055
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    13865061..13865498
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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