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LOC119230225 IFNAR1 promoter region [ Homo sapiens (human) ]

Gene ID: 119230225, updated on 12-Sep-2024

Summary

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Gene symbol
LOC119230225
Gene description
IFNAR1 promoter region
Gene type
biological region
Feature type(s)
protein_bind
regulatory: enhancer, promoter, 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 alpha and beta receptor subunit 1 (IFNAR1) gene, which encodes an antiviral factor that may play a role in interferon immunity in coronavirus disease 2019 (COVID-19). This region functions as a promoter that drives IFNAR1 expression. It includes a binding site for the high mobility group box 1 (HMGB1) protein, which together with poly(ADP-ribose) polymerase 1 (PARP-1), functions as a cofactor for IFNAR1 transcription, and where suppression of PARP-1 by hepatitis B virus infection can lower IFNAR1 expression. Two subregions marked by the H3K27ac histone modification were also shown to be active enhancers by ChIP-STARR-seq in human embryonic stem cells. Multiple polymorphisms have been found within this promoter, including a SNP (rs2850015) that affects promoter activity in HepG2 liver carcinoma cells, a GT(n) variable number tandem repeat (rs36158718) that affects promoter activity in 293T embryonic kidney cells, and a SNP (rs2843710) that affects promoter activity in THP-1 monocytes infected with enterovirus 71. This locus also includes two accessible chromatin subregions that were validated as enhancers based on their 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]
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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See LOC119230225 in Genome Data Viewer
Location:
21q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (33323674..33325798)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (31695918..31698042)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (34695979..34698103)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene IFNAR2-IL10RB readthrough Neighboring gene interferon alpha and beta receptor subunit 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18371 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18372 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 IL10RB divergent transcript 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 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 IFNGR2 promoter region 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

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. Novel IFN-alpha receptor promoter polymorphisms. Muldoon J, et al. Genes Immun, 2001 May. PMID 11426326
  2. A high proportion of chromosome 21 promoter polymorphisms influence transcriptional activity. Buckland PR, et al. Gene Expr, 2004. PMID 15200235, Free PMC Article
  3. Utilizing genomic polymorphisms to personalize hepatitis C therapies. Rifai MA, et al. Curr Opin Organ Transplant, 2012 Apr. PMID 22414802
  4. Functional dissection of an IFN-alpha/beta receptor 1 promoter variant that confers higher risk to chronic hepatitis B virus infection. Zhou J, et al. J Hepatol, 2009 Aug. PMID 19501422
  5. The dinucleotide microsatellite polymorphism of the IFNAR1 gene promoter correlates with responsiveness of hepatitis C patients to interferon. Matsuyama N, et al. Hepatol Res, 2003 Mar. PMID 12697242

See all (17) 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 Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 18376
  • ATAC-STARR-seq lymphoblastoid active region 18377
  • H3K27ac hESC enhancer GRCh37_chr21:34696299-34697201
  • H3K27ac hESC enhancer GRCh37_chr21:34697202-34698103
  • IFNAR1 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_070953.2 

    Range
    101..2225
    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    33323674..33325798
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    31695918..31698042
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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