rs5743604

Homo sapiens
A>G
TLR1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0331 (9910/29912,GnomAD)
G=0408 (11892/29118,TOPMED)
G=0468 (2346/5008,1000G)
G=0242 (933/3854,ALSPAC)
G=0222 (822/3708,TWINSUK)
chr4:38799664 (GRCh38.p7) (4p14)
AD
GWASdb2
7   publication(s)
See rs on genome
35 Enhancers around
26 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 4NC_000004.12:g.38799664A>G
GRCh37.p13 chr 4NC_000004.11:g.38801285A>G
TLR1 RefSeqGeneNG_016228.1:g.10128T>C

Gene: TLR1, toll like receptor 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
TLR1 transcriptNM_003263.3:c.N/AIntron Variant
TLR1 transcript variant X1XM_005262662.4:c.N/AIntron Variant
TLR1 transcript variant X5XM_011513742.2:c.N/AIntron Variant
TLR1 transcript variant X6XM_011513743.2:c.N/AIntron Variant
TLR1 transcript variant X8XM_011513744.2:c.N/AIntron Variant
TLR1 transcript variant X9XM_011513745.2:c.N/AIntron Variant
TLR1 transcript variant X2XM_017008571.1:c.N/AIntron Variant
TLR1 transcript variant X7XM_017008572.1:c.N/AIntron Variant
TLR1 transcript variant X3XR_925163.2:n.N/AIntron Variant
TLR1 transcript variant X4XR_925165.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.377G=0.623
1000GenomesAmericanSub694A=0.560G=0.440
1000GenomesEast AsianSub1008A=0.472G=0.528
1000GenomesEuropeSub1006A=0.726G=0.274
1000GenomesGlobalStudy-wide5008A=0.532G=0.468
1000GenomesSouth AsianSub978A=0.580G=0.420
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.758G=0.242
The Genome Aggregation DatabaseAfricanSub8702A=0.434G=0.566
The Genome Aggregation DatabaseAmericanSub836A=0.540G=0.460
The Genome Aggregation DatabaseEast AsianSub1608A=0.476G=0.524
The Genome Aggregation DatabaseEuropeSub18464A=0.803G=0.196
The Genome Aggregation DatabaseGlobalStudy-wide29912A=0.668G=0.331
The Genome Aggregation DatabaseOtherSub302A=0.570G=0.430
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.591G=0.408
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.778G=0.222
PMID Title Author Journal
19505919Toll-like receptor signaling pathway variants and prostate cancer mortality.Stark JRCancer Epidemiol Biomarkers Prev
20200442Sequence variants in the TLR4 and TLR6-1-10 genes and prostate cancer risk. Results based on pooled analysis from three independent studies.Lindstrom SCancer Epidemiol Biomarkers Prev
22359464Are Toll-like receptor gene polymorphisms associated with prostate cancer?Kutikhin AGCancer Manag Res
23743675A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.Kapoor MHum Genet
22150367Genetic variation in the Toll-like receptor gene cluster (TLR10-TLR1-TLR6) influences disease course in sarcoidosis.Veltkamp MTissue Antigens
24281113Inflammatory genetic markers of prostate cancer risk.Tindall EACancers (Basel)
18396467Genetic variation and haplotype structures of innate immunity genes in eastern India.Bairagya BBInfect Genet Evol

P-Value

SNP ID p-value Traits Study
rs57436044.09E-06alcohol consumption23743675

eQTL of rs5743604 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 rs5743604 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 )
chr43876089838761605E067-39680
chr43875394338755431E068-45854
chr43876089838761605E069-39680
chr43875307438753285E071-48000
chr43875333838753545E071-47740
chr43875356438753626E071-47659
chr43875394338755431E071-45854
chr43875968438759867E071-41418
chr43876089838761605E071-39680
chr43876222738762320E071-38965
chr43876407238764727E071-36558
chr43880262538802717E0711340
chr43880272438802921E0711439
chr43880308438803124E0711799
chr43881807538818437E07116790
chr43881856438818649E07117279
chr43876089838761605E072-39680
chr43876172238761850E072-39435
chr43876190738761976E072-39309
chr43876222738762320E072-38965
chr43881807538818437E07216790
chr43875333838753545E074-47740
chr43875356438753626E074-47659
chr43875957638759666E074-41619
chr43875968438759867E074-41418
chr43876089838761605E074-39680
chr43876172238761850E074-39435
chr43876190738761976E074-39309
chr43876222738762320E074-38965
chr43877100638771202E074-30083
chr43875158138751637E081-49648
chr43875163938751719E081-49566
chr43875394338755431E081-45854
chr43875158138751637E082-49648
chr43875163938751719E082-49566








Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr43880566838807737E0674383
chr43880436838804525E0683083
chr43880467738804759E0683392
chr43880523438805284E0683949
chr43880566838807737E0684383
chr43880523438805284E0693949
chr43880566838807737E0694383
chr43880403138804077E0712746
chr43880417738804308E0712892
chr43880436838804525E0713083
chr43880467738804759E0713392
chr43880523438805284E0713949
chr43880566838807737E0714383
chr43880436838804525E0723083
chr43880467738804759E0723392
chr43880523438805284E0723949
chr43880566838807737E0724383
chr43880467738804759E0733392
chr43880523438805284E0733949
chr43880566838807737E0734383
chr43880403138804077E0742746
chr43880417738804308E0742892
chr43880436838804525E0743083
chr43880467738804759E0743392
chr43880523438805284E0743949
chr43880566838807737E0744383