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LOC112543448 CRISPRi-FlowFISH-validated WDR83OS regulatory elements [ Homo sapiens (human) ]

Gene ID: 112543448, updated on 4-Mar-2025

Summary

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Gene symbol
LOC112543448
Gene description
CRISPRi-FlowFISH-validated WDR83OS regulatory elements
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project, and by an activity-by-contact (ABC) model that predicts enhancer-gene connections. Two subregions were validated as positively-acting cis-regulatory elements for the WDR83OS (WD repeat domain 83 opposite strand) gene based on CRISPR/Cas9-mediated perturbation (CRISPRi-FlowFISH method) in K562 cells. Two other subregions were validated as active enhancers by ChIP-STARR-seq in human embryonic stem cells, where both are associated with the NANOG transcription factor and are marked by the H3K27ac and H3K4me1 histone modifications. Another subregion was validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 1:Tss). [provided by RefSeq, Nov 2022]
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Genomic context

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See LOC112543448 in Genome Data Viewer
Location:
19p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (12681111..12682577)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (12805611..12807076)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (12791925..12793391)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14063 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10155 Neighboring gene mannosidase alpha class 2B member 1 Neighboring gene MPRA-validated peak3365 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:12775226-12776174 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:12776175-12777122 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14069 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14070 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:12781177-12781850 Neighboring gene WD repeat domain 83 opposite strand Neighboring gene WD repeat domain 83 Neighboring gene CRISPRi-FlowFISH-validated DHPS regulatory element Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14071 Neighboring gene deoxyhypusine synthase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:12793915-12794437 Neighboring gene G protein subunit gamma 14 Neighboring gene F-box and WD repeat domain containing 9 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14072

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. Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations. Fulco CP, et al. Nat Genet, 2019 Dec. PMID 31784727, 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. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:12792345-12792868
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:12792869-12793391
  • Sharpr-MPRA regulatory region 9902

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_057396.3 

    Range
    101..1567
    Download
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    12681111..12682577
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    12805611..12807076
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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