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LOC123575673 CRISPRi-FlowFISH-validated CD83 regulatory elements GRCh37_chr6:14117366-14118274 to GRCh37_chr6:14117614-14118430 [ Homo sapiens (human) ]

Gene ID: 123575673, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123575673
Gene description
CRISPRi-FlowFISH-validated CD83 regulatory elements GRCh37_chr6:14117366-14118274 to GRCh37_chr6:14117614-14118430
Gene type
biological region
Feature type(s)
regulatory: silencer, 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 was predicted to be an enhancer based on an activity-by-contact (ABC) model that predicts enhancer-gene connections, where the putative enhancer strength is measured by DNase I hypersensitivity and H3K27 acetylation, and the contact frequency by Hi-C. Three overlapping subregions were validated as positively-acting cis-regulatory elements for the CD83 (CD83 molecule) gene based on CRISPR/Cas9-mediated perturbation (CRISPRi-FlowFISH method) in either unstimulated or anti-CD3- and PMA-stimulated Jurkat T cells, or GM12878 lymphoblastoid cells. Another subregion was validated as a functional repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC123575673 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 (14117098..14118199)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (13989563..13990652)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (14117329..14117623)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374939 Neighboring gene CRISPRi-validated cis-regulatory element chr6.709 Neighboring gene uncharacterized LOC124901265 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 CD83 molecule Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:14128774-14129372 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24048 Neighboring gene RNA, U7 small nuclear 133 pseudogene Neighboring gene MPRA-validated peak5669 silencer Neighboring gene uncharacterized LOC105374940

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. Genome-wide enhancer maps link risk variants to disease genes. Nasser J, et al. Nature, 2021 May. PMID 33828297, Free PMC Article
  2. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article
  3. 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 silent region 16942
  • CRISPRi-FlowFISH-validated CD83 regulatory element GRCh37_chr6:14117366-14118274
  • CRISPRi-FlowFISH-validated CD83 regulatory element GRCh37_chr6:14117614-14118269
  • CRISPRi-FlowFISH-validated CD83 regulatory element GRCh37_chr6:14117614-14118430
  • Sharpr-MPRA regulatory region 13983

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_077932.2 

    Range
    101..1202
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    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
    14117098..14118199
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    13989563..13990652
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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