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LOC119266102 IFNGR2 promoter region [ Homo sapiens (human) ]

Gene ID: 119266102, updated on 10-Oct-2023

Summary

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Gene symbol
LOC119266102
Gene description
IFNGR2 promoter region
Gene type
biological region
Feature type(s)
protein_bind
regulatory: promoter, 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 represents the 5' regulatory region of the interferon gamma receptor 2 (IFNGR2) gene, which is located in a chromosome 21q22 interferon receptor gene cluster that represents a susceptibility locus for severe coronavirus disease 2019 (COVID-19). This region functions as a promoter that drives IFNGR2 expression. It includes a motif that can bind nuclear factor kappa B (NF-kB) subunits, which may function in the up-regulation of IFNGR2 by Bryostatin-1 in monocytes. Multiple polymorphisms have been found within this promoter, including the SNPs rs8134145, rs8126756 and rs17882748, which show significantly increased promoter activity when combinatorially present in an ATC haplotype. Two subregions were validated as cis-regulatory elements for IFNGR2 based on CRISPR/Cas9-mediated perturbation (CRISPRi-FlowFISH method), where one was a positively-acting element in GM12878 lymphoblastoid cells, and the other was a negatively-acting element in THP-1 monocytic cells. 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) massively parallel reporter assay (MPRA) in GM12878 cells. [provided by RefSeq, May 2023]
Annotation information
Note: This locus has been reviewed for its involvement in coronavirus biology, and is involved in host gene regulation.
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Genomic context

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Location:
21q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (33401958..33403631)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (31774212..31775892)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (34774667..34775844)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene IFNAR2-IL10RB readthrough Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18373 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18374 Neighboring gene interleukin 10 receptor subunit beta Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18375 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:34676441-34676940 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13255 Neighboring gene IFNAR1 promoter region Neighboring gene interferon alpha and beta receptor subunit 1 Neighboring gene upstream transcription factor 1 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 14728 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr21:34738709-34739908 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr21:34752348-34753547 Neighboring gene Sharpr-MPRA regulatory region 6397 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:34758349-34758554 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13257 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13258 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13259 Neighboring gene CRISPRi-FlowFISH-validated IFNGR2 regulatory element GRCh37_chr21:34776289-34777452 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:34784507-34785261 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:34785395-34785563 Neighboring gene interferon gamma receptor 2 Neighboring gene transmembrane protein 50B Neighboring gene RPS5 pseudogene 3

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. No significant impact of IFN-γ pathway gene variants on tuberculosis susceptibility in a West African population. Meyer CG, et al. Eur J Hum Genet, 2016 May. PMID 26242990, Free PMC Article
  2. Differential DNA methylation status between breast carcinomatous and normal tissues. Wang F, et al. Biomed Pharmacother, 2014 Jul. PMID 25070394
  3. A new epigenetic challenge: systemic lupus erythematosus. Javierre BM, et al. Adv Exp Med Biol, 2011. PMID 21627046
  4. The antineoplastic agent bryostatin-1 differentially regulates IFN-gamma receptor subunits in monocytic cells: transcriptional and posttranscriptional control of IFN-gamma R2. Garcia CS, et al. J Immunol, 2006 Aug 15. PMID 16888033
  5. Association of IFNGR2 gene polymorphisms with pulmonary tuberculosis among the Vietnamese. Hijikata M, et al. Hum Genet, 2012 May. PMID 22057826, Free PMC Article

See all (8) citations in PubMed

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 13256
  • CRISPRi-FlowFISH-validated IFNGR2 regulatory element GRCh37_chr21:34774264-34775451
  • CRISPRi-FlowFISH-validated IFNGR2 regulatory element GRCh37_chr21:34774836-34775451
  • IFNGR2 5' regulatory region

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_070955.3 

    Range
    101..1774
    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    33401958..33403631
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    31774212..31775892
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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