LOC119230225 (IFNAR1 promoter region) - Rat Genome Database

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Gene: LOC119230225 (IFNAR1 promoter region) Homo sapiens
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Symbol: LOC119230225
Name: IFNAR1 promoter region
RGD ID: 40818287
Description: 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]
Type: biological-region
RefSeq Status: REVIEWED
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
NCBI Annotation Information: Note: This locus has been reviewed for its involvement in coronavirus biology, and is involved in host gene regulation.
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382133,323,674 - 33,325,798 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372134,695,979 - 34,698,103 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map21qNCBI
T2T-CHM13v2.02131,695,918 - 31,698,042 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
ZTTK syndrome  (IAGP)

References
Additional References at PubMed
PMID:11426326   PMID:12697242   PMID:12761564   PMID:15200235   PMID:15990456   PMID:16338279   PMID:17125879   PMID:18761606   PMID:19501422   PMID:22414802   PMID:25445652   PMID:25939635  
PMID:26679744   PMID:29713327   PMID:30033119   PMID:30383464   PMID:35858748  


Genomics

Variants

.
Variants in LOC119230225
21 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 21q22.11-22.3(chr21:7749532-46670346)x3 copy number gain See cases [RCV000135310] Chr21:7749532..46670346 [GRCh38]
Chr21:34111831..48090258 [GRCh37]
Chr21:33033702..46914686 [NCBI36]
Chr21:21q22.11-22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46664250)x3 copy number gain See cases [RCV000134836] Chr21:7749532..46664250 [GRCh38]
Chr21:15485038..48084162 [GRCh37]
Chr21:14406909..46908590 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46660999)x3 copy number gain See cases [RCV000135448] Chr21:7749532..46660999 [GRCh38]
Chr21:15499847..48080911 [GRCh37]
Chr21:14421718..46905339 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46670405)x3 copy number gain See cases [RCV000148131] Chr21:7749532..46670405 [GRCh38]
Chr21:15499847..48090317 [GRCh37]
Chr21:14421718..46914745 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46653084)x3 copy number gain See cases [RCV000134727] Chr21:7749532..46653084 [GRCh38]
Chr21:15485038..48072996 [GRCh37]
Chr21:14406909..46897424 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-42971047)x3 copy number gain See cases [RCV000133676] Chr21:7749532..42971047 [GRCh38]
Chr21:15499847..44391157 [GRCh37]
Chr21:14421718..43264226 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46670440)x3 copy number gain See cases [RCV000134119] Chr21:7749532..46670440 [GRCh38]
Chr21:15485038..48090352 [GRCh37]
Chr21:14406909..46914780 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7817158-46670440)x1 copy number loss See cases [RCV000142427] Chr21:7817158..46670440 [GRCh38]
Chr21:15485038..48090352 [GRCh37]
Chr21:14406909..46914780 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21q11.2-22.3(chr21:7749532-46677460) copy number gain See cases [RCV000143160] Chr21:7749532..46677460 [GRCh38]
Chr21:14386013..48097372 [GRCh37]
Chr21:13307884..46921800 [NCBI36]
Chr21:21q11.2-22.3		 pathogenic
GRCh38/hg38 21q11.2-22.3(chr21:7749532-46677460)x3 copy number gain See cases [RCV000143376] Chr21:7749532..46677460 [GRCh38]
Chr21:15006458..48097372 [GRCh37]
Chr21:13928329..46921800 [NCBI36]
Chr21:21q11.2-22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46670405)x3 copy number gain See cases [RCV000050445] Chr21:7749532..46670405 [GRCh38]
Chr21:15499847..48090317 [GRCh37]
Chr21:14421718..46914745 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic|conflicting interpretations of pathogenicity|conflicting data from submitters
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46623792)x3 copy number gain See cases [RCV000053039] Chr21:7749532..46623792 [GRCh38]
Chr21:14524963..48043704 [GRCh37]
Chr21:13446834..46868132 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46623792)x3 copy number gain See cases [RCV000053042] Chr21:7749532..46623792 [GRCh38]
Chr21:14595524..48043704 [GRCh37]
Chr21:13517395..46868132 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46623792)x3 copy number gain See cases [RCV000053043] Chr21:7749532..46623792 [GRCh38]
Chr21:14629063..48043704 [GRCh37]
Chr21:13550934..46868132 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46670546)x3 copy number gain See cases [RCV000053045] Chr21:7749532..46670546 [GRCh38]
Chr21:15499647..48090458 [GRCh37]
Chr21:14421518..46914886 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46661140)x3 copy number gain See cases [RCV000053067] Chr21:7749532..46661140 [GRCh38]
Chr21:15499847..48081052 [GRCh37]
Chr21:14421718..46905480 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46670440)x3 copy number gain See cases [RCV000134842] Chr21:7749532..46670440 [GRCh38]
Chr21:15513244..48090352 [GRCh37]
Chr21:14435115..46914780 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21q11.2-22.3(chr21:7749532-46649831)x3 copy number gain See cases [RCV000134509] Chr21:7749532..46649831 [GRCh38]
Chr21:14577835..48069743 [GRCh37]
Chr21:13499706..46894171 [NCBI36]
Chr21:21q11.2-22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46653090)x3 copy number gain See cases [RCV000053040] Chr21:7749532..46653090 [GRCh38]
Chr21:14539679..48073002 [GRCh37]
Chr21:13461550..46897430 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46661140)x3 copy number gain See cases [RCV000053065] Chr21:7749532..46661140 [GRCh38]
Chr21:15499647..48081052 [GRCh37]
Chr21:14421518..46905480 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46670405)x3 copy number gain See cases [RCV000053069] Chr21:7749532..46670405 [GRCh38]
Chr21:34423268..48090317 [GRCh37]
Chr21:33345138..46914745 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21q21.3-22.3(chr21:7749532-46677460)x3 copy number gain See cases [RCV000141827] Chr21:7749532..46677460 [GRCh38]
Chr21:28285299..48097372 [GRCh37]
Chr21:27207170..46921800 [NCBI36]
Chr21:21q21.3-22.3		 uncertain significance
GRCh38/hg38 21q11.2-22.3(chr21:7749532-46677460)x3 copy number gain See cases [RCV000143120] Chr21:7749532..46677460 [GRCh38]
Chr21:15006457..48097372 [GRCh37]
Chr21:13928328..46921800 [NCBI36]
Chr21:21q11.2-22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46670405)x3 copy number gain See cases [RCV000053068] Chr21:7749532..46670405 [GRCh38]
Chr21:20655360..48090317 [GRCh37]
Chr21:19577231..46914745 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46671060)x3 copy number gain See cases [RCV000137255] Chr21:7749532..46671060 [GRCh38]
Chr21:35319225..48090972 [GRCh37]
Chr21:34241095..46915400 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21q11.2-22.3(chr21:7749532-46670346)x3 copy number gain See cases [RCV000140103] Chr21:7749532..46670346 [GRCh38]
Chr21:14577894..48090258 [GRCh37]
Chr21:13499765..46914686 [NCBI36]
Chr21:21q11.2-22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46671060)x3 copy number gain See cases [RCV000137337] Chr21:7749532..46671060 [GRCh38]
Chr21:10697897..48090972 [GRCh37]
Chr21:1..46915400 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.13(chr21:7749532-37653653)x1 copy number loss See cases [RCV000138095] Chr21:7749532..37653653 [GRCh38]
Chr21:15451032..39025955 [GRCh37]
Chr21:14372903..37947825 [NCBI36]
Chr21:21p11.2-q22.13		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46671060)x3 copy number gain See cases [RCV000138216] Chr21:7749532..46671060 [GRCh38]
Chr21:10944001..48090972 [GRCh37]
Chr21:9965872..46915400 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46671060)x3 copy number gain See cases [RCV000138436] Chr21:7749532..46671060 [GRCh38]
Chr21:15451032..48090972 [GRCh37]
Chr21:14372903..46915400 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic|conflicting data from submitters
GRCh38/hg38 21q11.2-22.3(chr21:7749532-46698247)x3 copy number gain See cases [RCV000141346] Chr21:7749532..46698247 [GRCh38]
Chr21:14577835..48118159 [GRCh37]
Chr21:13499706..46942587 [NCBI36]
Chr21:21q11.2-22.3		 pathogenic
Single allele deletion ZTTK syndrome [RCV002247722] Chr21:32213458..34373118 [GRCh38]
Chr21:21q22.11		 pathogenic
NM_000629.3(IFNAR1):c.31C>G (p.Leu11Val) single nucleotide variant not provided [RCV001940863] Chr21:33325086 [GRCh38]
Chr21:34697391 [GRCh37]
Chr21:21q22.11		 uncertain significance
NM_000629.3(IFNAR1):c.69A>G (p.Ala23=) single nucleotide variant not provided [RCV002607825] Chr21:33325124 [GRCh38]
Chr21:34697429 [GRCh37]
Chr21:21q22.11		 likely benign
NM_000629.3(IFNAR1):c.36G>C (p.Val12=) single nucleotide variant not provided [RCV002107330] Chr21:33325091 [GRCh38]
Chr21:34697396 [GRCh37]
Chr21:21q22.11		 likely benign
NM_000629.3(IFNAR1):c.55T>G (p.Trp19Gly) single nucleotide variant not provided [RCV001876300] Chr21:33325110 [GRCh38]
Chr21:34697415 [GRCh37]
Chr21:21q22.11		 uncertain significance
NM_000629.3(IFNAR1):c.24G>A (p.Ala8=) single nucleotide variant not provided [RCV002829549] Chr21:33325079 [GRCh38]
Chr21:34697384 [GRCh37]
Chr21:21q22.11		 likely benign
NM_000629.3(IFNAR1):c.17T>C (p.Leu6Pro) single nucleotide variant not provided [RCV002033813] Chr21:33325072 [GRCh38]
Chr21:34697377 [GRCh37]
Chr21:21q22.11		 uncertain significance
NM_000629.3(IFNAR1):c.14T>G (p.Leu5Arg) single nucleotide variant not provided [RCV002598495] Chr21:33325069 [GRCh38]
Chr21:34697374 [GRCh37]
Chr21:21q22.11		 uncertain significance
NM_000629.3(IFNAR1):c.46G>A (p.Val16Met) single nucleotide variant not provided [RCV001989289] Chr21:33325101 [GRCh38]
Chr21:34697406 [GRCh37]
Chr21:21q22.11		 uncertain significance
NM_000629.3(IFNAR1):c.28A>G (p.Thr10Ala) single nucleotide variant not provided [RCV001920296]|not specified [RCV004043304] Chr21:33325083 [GRCh38]
Chr21:34697388 [GRCh37]
Chr21:21q22.11		 likely benign|uncertain significance
NM_000629.3(IFNAR1):c.65CCGCAG[1] (p.Ala24_Ala25del) microsatellite not provided [RCV001916620] Chr21:33325120..33325125 [GRCh38]
Chr21:34697425..34697430 [GRCh37]
Chr21:21q22.11		 uncertain significance
NM_000629.3(IFNAR1):c.50C>T (p.Ala17Val) single nucleotide variant not provided [RCV002862365]|not specified [RCV004064980] Chr21:33325105 [GRCh38]
Chr21:34697410 [GRCh37]
Chr21:21q22.11		 uncertain significance
NM_000629.3(IFNAR1):c.10G>A (p.Val4Ile) single nucleotide variant not provided [RCV003040244] Chr21:33325065 [GRCh38]
Chr21:34697370 [GRCh37]
Chr21:21q22.11		 uncertain significance
NM_000629.3(IFNAR1):c.76+9C>A single nucleotide variant not provided [RCV003014445] Chr21:33325140 [GRCh38]
Chr21:34697445 [GRCh37]
Chr21:21q22.11		 likely benign
NM_000629.3(IFNAR1):c.36G>A (p.Val12=) single nucleotide variant not provided [RCV001463407] Chr21:33325091 [GRCh38]
Chr21:34697396 [GRCh37]
Chr21:21q22.11		 likely benign
NM_000629.3(IFNAR1):c.27del (p.Thr10fs) deletion not provided [RCV002904554] Chr21:33325082 [GRCh38]
Chr21:34697387 [GRCh37]
Chr21:21q22.11		 pathogenic
NM_000629.3(IFNAR1):c.64T>G (p.Ser22Ala) single nucleotide variant not provided [RCV003547199] Chr21:33325119 [GRCh38]
Chr21:34697424 [GRCh37]
Chr21:21q22.11		 uncertain significance
NM_000629.3(IFNAR1):c.76+10G>A single nucleotide variant not provided [RCV003703578] Chr21:33325141 [GRCh38]
Chr21:34697446 [GRCh37]
Chr21:21q22.11		 likely benign
NM_000629.3(IFNAR1):c.72C>T (p.Ala24=) single nucleotide variant not provided [RCV003558070] Chr21:33325127 [GRCh38]
Chr21:34697432 [GRCh37]
Chr21:21q22.11		 likely benign
NM_000629.3(IFNAR1):c.15C>A (p.Leu5=) single nucleotide variant not provided [RCV003668977] Chr21:33325070 [GRCh38]
Chr21:34697375 [GRCh37]
Chr21:21q22.11		 likely benign
NM_000629.3(IFNAR1):c.18G>A (p.Leu6=) single nucleotide variant not provided [RCV003848181] Chr21:33325073 [GRCh38]
Chr21:34697378 [GRCh37]
Chr21:21q22.11		 likely benign
NM_000629.3(IFNAR1):c.16C>T (p.Leu6=) single nucleotide variant not provided [RCV002119295] Chr21:33325071 [GRCh38]
Chr21:34697376 [GRCh37]
Chr21:21q22.11		 likely benign
NM_000629.3(IFNAR1):c.76+7G>A single nucleotide variant not provided [RCV002160571] Chr21:33325138 [GRCh38]
Chr21:34697443 [GRCh37]
Chr21:21q22.11		 likely benign
NM_000629.3(IFNAR1):c.21C>T (p.Gly7=) single nucleotide variant not provided [RCV002766176] Chr21:33325076 [GRCh38]
Chr21:34697381 [GRCh37]
Chr21:21q22.11		 likely benign

QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
407178870GWAS827846_Hmultiple sclerosis QTL GWAS827846 (human)0.000008multiple sclerosis213332387633323877Human
407258866GWAS907842_Hinterferon alpha/beta receptor 1 measurement QTL GWAS907842 (human)1e-51interferon alpha/beta receptor 1 measurement213332567633325677Human
2303081MAMTS49_HMammary tumor susceptibility QTL 49 (human)1.72Mammary tumor susceptibility211795044843950448Human


Expression

RNA-SEQ Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC119230225 COSMIC
GTEx LOC119230225 GTEx
Human Proteome Map LOC119230225 Human Proteome Map
NCBI Gene LOC119230225 ENTREZGENE