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LOC123038178 Sharpr-MPRA regulatory region 8233 [ Homo sapiens (human) ]

Gene ID: 123038178, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123038178
Gene description
Sharpr-MPRA regulatory region 8233
Gene type
biological region
Feature type(s)
regulatory: silencer
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. It 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 non-DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). A genetic variant at this locus, rs62266860, may be associated with coronavirus disease 2019 (COVID-19) pneumonia. [provided by RefSeq, Dec 2022]
Annotation information
Note: This locus has been reviewed for its involvement in coronavirus biology, and is locus in the vicinity of disease-associated variant(s).
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Genomic context

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See LOC123038178 in Genome Data Viewer
Location:
3q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (129228966..129229260)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (131973781..131974075)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (128947809..128948103)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374101 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20506 Neighboring gene NFE2L2 motif-containing MPRA enhancer 136 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:128931398-128931601 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:128937355-128938310 Neighboring gene ribosomal protein S27 pseudogene 12 Neighboring gene uncharacterized LOC105374102 Neighboring gene NANOG hESC enhancer GRCh37_chr3:128950251-128950752 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20507 Neighboring gene CRISPRi-FlowFISH-validated H1-10 regulatory element 3 Neighboring gene COPI coat complex subunit gamma 1 Neighboring gene microRNA 6826

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. Trans-ancestry analysis reveals genetic and nongenetic associations with COVID-19 susceptibility and severity. Shelton JF, et al. Nat Genet, 2021 Jun. PMID 33888907
  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

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_077309.1 

    Range
    101..395
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    129228966..129229260
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    131973781..131974075
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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