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LOC116158544 CRISPRi-validated cis-regulatory element chr6.709 [ Homo sapiens (human) ]

Gene ID: 116158544, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116158544
Gene description
CRISPRi-validated cis-regulatory element chr6.709
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. It was validated as a high-confidence cis-regulatory element for the CD83 (CD83 molecule) gene on chromosome 6 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:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (14108628..14109415)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (13981091..13981878)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (14108859..14109646)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes 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 CRISPRi-validated cis-regulatory element chr6.704 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 uncharacterized LOC124901265 Neighboring gene CRISPRi-FlowFISH-validated CD83 regulatory elements GRCh37_chr6:14117366-14118274 to GRCh37_chr6:14117614-14118430 Neighboring gene CRISPRi-FlowFISH-validated CD83 regulatory elements GRCh37_chr6:14118435-14118935 to GRCh37_chr6:14118800-14119300 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24046 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24047 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:14128774-14129372 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24048 Neighboring gene CD83 molecule Neighboring gene RNA, U7 small nuclear 133 pseudogene

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 24045

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_066685.1 

    Range
    101..888
    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
    14108628..14109415
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    13981091..13981878
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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