rs729302

Homo sapiens
A>C
None
Check p-value
SNV (Single Nucleotide Variation)
C=0282 (8425/29858,GnomAD)
C=0265 (7737/29118,TOPMED)
C=0262 (1314/5008,1000G)
C=0322 (1241/3854,ALSPAC)
C=0331 (1226/3708,TWINSUK)
chr7:128928906 (GRCh38.p7) (7q32.1)
AD
GWASdb2
See rs on genome

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 7NC_000007.14:g.128928906A>C
GRCh37.p13 chr 7NC_000007.13:g.128568960A>C

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.818C=0.182
1000GenomesAmericanSub694A=0.810C=0.190
1000GenomesEast AsianSub1008A=0.683C=0.317
1000GenomesEuropeSub1006A=0.674C=0.326
1000GenomesGlobalStudy-wide5008A=0.738C=0.262
1000GenomesSouth AsianSub978A=0.700C=0.300
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.678C=0.322
The Genome Aggregation DatabaseAfricanSub8704A=0.810C=0.190
The Genome Aggregation DatabaseAmericanSub834A=0.800C=0.200
The Genome Aggregation DatabaseEast AsianSub1614A=0.685C=0.315
The Genome Aggregation DatabaseEuropeSub18404A=0.673C=0.327
The Genome Aggregation DatabaseGlobalStudy-wide29858A=0.717C=0.282
The Genome Aggregation DatabaseOtherSub302A=0.750C=0.250
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.734C=0.265
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.669C=0.331
PMID Title Author Journal
17412832Three functional variants of IFN regulatory factor 5 (IRF5) define risk and protective haplotypes for human lupus.Graham RRProc Natl Acad Sci U S A
18285424Interferon regulatory factor 5 (IRF5) gene variants are associated with multiple sclerosis in three distinct populations.Kristjansdottir GJ Med Genet
22544929IRF5 risk polymorphisms contribute to interindividual variance in pattern recognition receptor-mediated cytokine secretion in human monocyte-derived cells.Hedl MJ Immunol
19440200Identification of new SLE-associated genes with a two-step Bayesian study design.Armstrong DLGenes Immun
25337792Genetic association study of TNFAIP3, IFIH1, IRF5 polymorphisms with polymyositis/dermatomyositis in Chinese Han population.Chen SPLoS One
19228650Association of polymorphisms in interferon regulatory factor 5 gene with rheumatoid arthritis: a metaanalysis.Han SWJ Rheumatol
20453842Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci.Stahl EANat Genet
23073787Associations between interferon regulatory factor 5 polymorphisms and rheumatoid arthritis: a meta-analysis.Lee YHMol Biol Rep
21898142Association of IRF5 polymorphisms with susceptibility to hemophagocytic lymphohistiocytosis in children.Yanagimachi MJ Clin Immunol
18408250A single nucleotide polymorphism in the IRF5 promoter region is associated with susceptibility to rheumatoid arthritis in the Japanese population.Shimane KAnn Rheum Dis
21239750Association of IRF5 polymorphisms with susceptibility to macrophage activation syndrome in patients with juvenile idiopathic arthritis.Yanagimachi MJ Rheumatol
23049788Further evidence of subphenotype association with systemic lupus erythematosus susceptibility loci: a European cases only study.Alonso-Perez EPLoS One
20662065Identification of candidate loci at 6p21 and 21q22 in a genome-wide association study of cardiac manifestations of neonatal lupus.Clancy RMArthritis Rheum
20479942Genetic risk factors in lupus nephritis and IgA nephropathy--no support of an overlap.Vuong MTPLoS One
20169177Genome-wide association study in Asian populations identifies variants in ETS1 and WDFY4 associated with systemic lupus erythematosus.Yang WPLoS Genet
19581569Genome-wide association study of alcohol dependence.Treutlein JArch Gen Psychiatry
21834935A meta-analysis of the association of IRF5 polymorphism with systemic lupus erythematosus.Hu WInt J Immunogenet
22162633Activation of type I interferon pathway in systemic lupus erythematosus: association with distinct clinical phenotypes.Karageorgas TPJ Biomed Biotechnol
23941291Identification of three new cis-regulatory IRF5 polymorphisms: in vitro studies.Alonso-Perez EArthritis Res Ther
17568788Opposed independent effects and epistasis in the complex association of IRF5 to SLE.Ferreiro-Neira IGenes Immun
17389033Replication of the genetic effects of IFN regulatory factor 5 (IRF5) on systemic lupus erythematosus in a Korean population.Shin HDArthritis Res Ther
21627826Cis-regulation of IRF5 expression is unable to fully account for systemic lupus erythematosus association: analysis of multiple experiments with lymphoblastoid cell lines.Alonso-Perez EArthritis Res Ther
18063667Comprehensive evaluation of the genetic variants of interferon regulatory factor 5 (IRF5) reveals a novel 5 bp length polymorphism as strong risk factor for systemic lupus erythematosus.Sigurdsson SHum Mol Genet
22541939Bias in effect size of systemic lupus erythematosus susceptibility loci across Europe: a case-control study.Alonso-Perez EArthritis Res Ther
24946689Lack of replication of higher genetic risk load in men than in women with systemic lupus erythematosus.Alonso-Perez EArthritis Res Ther
15657875Polymorphisms in the tyrosine kinase 2 and interferon regulatory factor 5 genes are associated with systemic lupus erythematosus.Sigurdsson SAm J Hum Genet
23288367Interferon regulatory factor 5 polymorphisms in sarcoidosis.Tanizawa KMod Rheumatol
20881011Early disease onset is predicted by a higher genetic risk for lupus and is associated with a more severe phenotype in lupus patients.Webb RAnn Rheum Dis
22110124Analysis of autosomal genes reveals gene-sex interactions and higher total genetic risk in men with systemic lupus erythematosus.Hughes TAnn Rheum Dis

P-Value

SNP ID p-value Traits Study
rs7293024.62E-05alcohol dependence19581569

eQTL of rs729302 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
There is no eQTL annotation for this SNP

meQTL of rs729302 in Fetal Brain

Probe ID Position Gene beta p-value
There is no meQTL annotation for this SNP

Genomic View

Chromatin Interaction

There is no significant Hi-C chromatin interaction data for this SNP.

Enhancer Annotation (GRCh37.p13)

Chromosome Start End Region Distance ( -/+ : Up/Downstream )
chr7128519758128520734E067-48226
chr7128520762128520906E067-48054
chr7128588390128588660E06819430
chr7128588688128588881E06819728
chr7128544551128545117E069-23843
chr7128560389128560458E069-8502
chr7128519758128520734E070-48226
chr7128520762128520906E070-48054
chr7128521007128521284E070-47676
chr7128519758128520734E071-48226
chr7128551415128552102E071-16858
chr7128587093128587158E07118133
chr7128587897128588305E07118937
chr7128588309128588373E07119349
chr7128588390128588660E07119430
chr7128588688128588881E07119728
chr7128519758128520734E072-48226
chr7128520762128520906E072-48054
chr7128519758128520734E073-48226
chr7128519758128520734E074-48226
chr7128588688128588881E07419728
chr7128519589128519705E081-49255
chr7128519758128520734E081-48226
chr7128527914128528030E081-40930
chr7128531811128532007E081-36953
chr7128532012128532072E081-36888
chr7128532129128532214E081-36746
chr7128558326128558453E081-10507
chr7128558772128558822E081-10138
chr7128560194128560338E081-8622
chr7128560389128560458E081-8502
chr7128519758128520734E082-48226
chr7128520762128520906E082-48054
chr7128521007128521284E082-47676
chr7128549165128549308E082-19652










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr7128577766128578186E0678806
chr7128578238128579111E0679278
chr7128577629128577734E0688669
chr7128577766128578186E0688806
chr7128555474128555737E069-13223
chr7128577629128577734E0698669
chr7128577766128578186E0698806
chr7128555474128555737E070-13223
chr7128556086128556167E070-12793
chr7128556195128556245E070-12715
chr7128577766128578186E0708806
chr7128578238128579111E0719278
chr7128577766128578186E0728806
chr7128577629128577734E0738669
chr7128577766128578186E0738806
chr7128578238128579111E0739278
chr7128555474128555737E074-13223
chr7128577629128577734E0748669
chr7128577766128578186E0748806
chr7128578238128579111E0749278
chr7128549331128551372E082-17588
chr7128555474128555737E082-13223
chr7128556086128556167E082-12793
chr7128556195128556245E082-12715
chr7128577629128577734E0828669
chr7128577766128578186E0828806