rs4543123

Homo sapiens
A>G
TLR1 : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0297 (8920/29958,GnomAD)
G=0367 (10694/29118,TOPMED)
G=0368 (1842/5008,1000G)
G=0238 (917/3854,ALSPAC)
G=0220 (815/3708,TWINSUK)
chr4:38790903 (GRCh38.p7) (4p14)
AD
GWASdb2
6   publication(s)
See rs on genome
38 Enhancers around
26 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 4NC_000004.12:g.38790903A>G
GRCh37.p13 chr 4NC_000004.11:g.38792524A>G

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

Molecule type Change Amino acid[Codon] SO Term
TLR1 transcriptNM_003263.3:c.N/AGenic Downstream Transcript Variant
TLR1 transcript variant X1XM_005262662.4:c.N/AGenic Downstream Transcript Variant
TLR1 transcript variant X5XM_011513742.2:c.N/AGenic Downstream Transcript Variant
TLR1 transcript variant X6XM_011513743.2:c.N/AGenic Downstream Transcript Variant
TLR1 transcript variant X8XM_011513744.2:c.N/AGenic Downstream Transcript Variant
TLR1 transcript variant X9XM_011513745.2:c.N/AGenic Downstream Transcript Variant
TLR1 transcript variant X2XM_017008571.1:c.N/AGenic Downstream Transcript Variant
TLR1 transcript variant X7XM_017008572.1:c.N/AGenic Downstream Transcript Variant
TLR1 transcript variant X4XR_925165.1:n.306...XR_925165.1:n.3064T>CT>CNon Coding Transcript Variant
TLR1 transcript variant X3XR_925163.2:n.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.467G=0.533
1000GenomesAmericanSub694A=0.780G=0.220
1000GenomesEast AsianSub1008A=0.591G=0.409
1000GenomesEuropeSub1006A=0.733G=0.267
1000GenomesGlobalStudy-wide5008A=0.632G=0.368
1000GenomesSouth AsianSub978A=0.690G=0.310
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.762G=0.238
The Genome Aggregation DatabaseAfricanSub8712A=0.494G=0.506
The Genome Aggregation DatabaseAmericanSub834A=0.800G=0.200
The Genome Aggregation DatabaseEast AsianSub1618A=0.614G=0.386
The Genome Aggregation DatabaseEuropeSub18492A=0.805G=0.194
The Genome Aggregation DatabaseGlobalStudy-wide29958A=0.702G=0.297
The Genome Aggregation DatabaseOtherSub302A=0.580G=0.420
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.632G=0.367
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.780G=0.220
PMID Title Author Journal
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
19503599The impact of divergence time on the nature of population structure: an example from Iceland.Price ALPLoS Genet
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
26019233Dissecting the genetics of the human transcriptome identifies novel trait-related trans-eQTLs and corroborates the regulatory relevance of non-protein coding locidagger.Kirsten HHum Mol Genet
23063165Associations and interactions of genetic polymorphisms in innate immunity genes with early viral infections and susceptibility to asthma and asthma-related phenotypes.Daley DJ Allergy Clin Immunol

P-Value

SNP ID p-value Traits Study
rs45431239E-06alcohol consumption23743675

eQTL of rs4543123 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr4:38792524TLR1ENSG00000174125.3A>G1.1602e-2-14675Caudate_basal_ganglia

meQTL of rs4543123 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 )
chr43876089838761605E067-30919
chr43875394338755431E068-37093
chr43876089838761605E069-30919
chr43875307438753285E071-39239
chr43875333838753545E071-38979
chr43875356438753626E071-38898
chr43875394338755431E071-37093
chr43875968438759867E071-32657
chr43876089838761605E071-30919
chr43876222738762320E071-30204
chr43876407238764727E071-27797
chr43880262538802717E07110101
chr43880272438802921E07110200
chr43880308438803124E07110560
chr43881807538818437E07125551
chr43881856438818649E07126040
chr43876089838761605E072-30919
chr43876172238761850E072-30674
chr43876190738761976E072-30548
chr43876222738762320E072-30204
chr43881807538818437E07225551
chr43875333838753545E074-38979
chr43875356438753626E074-38898
chr43875957638759666E074-32858
chr43875968438759867E074-32657
chr43876089838761605E074-30919
chr43876172238761850E074-30674
chr43876190738761976E074-30548
chr43876222738762320E074-30204
chr43877100638771202E074-21322
chr43874503938745146E081-47378
chr43875105738751361E081-41163
chr43875158138751637E081-40887
chr43875163938751719E081-40805
chr43875394338755431E081-37093
chr43875105738751361E082-41163
chr43875158138751637E082-40887
chr43875163938751719E082-40805








Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr43880566838807737E06713144
chr43880436838804525E06811844
chr43880467738804759E06812153
chr43880523438805284E06812710
chr43880566838807737E06813144
chr43880523438805284E06912710
chr43880566838807737E06913144
chr43880403138804077E07111507
chr43880417738804308E07111653
chr43880436838804525E07111844
chr43880467738804759E07112153
chr43880523438805284E07112710
chr43880566838807737E07113144
chr43880436838804525E07211844
chr43880467738804759E07212153
chr43880523438805284E07212710
chr43880566838807737E07213144
chr43880467738804759E07312153
chr43880523438805284E07312710
chr43880566838807737E07313144
chr43880403138804077E07411507
chr43880417738804308E07411653
chr43880436838804525E07411844
chr43880467738804759E07412153
chr43880523438805284E07412710
chr43880566838807737E07413144