Pathway

Pathway-based stratification of instruments

Trait

 

P-value threshold: 1e-5
   

 

 

 Summary

This is a pilot view to explore the potential of pathway data to inform us about groups of SNPs that may share pleiotropic relationships. For a trait we identify all SNPs that can be mapped to genes/proteins, and from those genes/proteins we look for common pathways.

Data sources

  • Gene/protein to pathway mappings from Reactome
  • MR estimates from MR-EvE (Hemani et al, Automating Mendelian randomization through machine learning to construct a putative causal map of the human phenome, bioRxiv 10.1101/173682)
  • SNP-trait assocaitions are from the IEU GWAS database

 How to use

Enter the trait you are interested in, the p-value threshold you want to use, then press "Search". You can adjust the slider and press Search again to update the results.

View the top results in the Network plot tab, access and search the full results in the Table tab, or use the Query tab to find out how to download data using the API.

 Examples

 Displays 94 / 94 paths

 

gwas.id gwas.trait mre_study_snp.beta mre_study_snp.se mre_study_snp.eaf mre_study_snp.pval mre_study_snp.samplesize snp.name gene.name protein.uniprot_id pathway.reactome_id pathway.name
300 LDL cholesterol -0.4853 0.0119 0.03166 1.000000e-200 139198.0 rs7254892 TOMM40 O96008 R-HSA-1268020 Mitochondrial protein import
300 LDL cholesterol -0.4853 0.0119 0.03166 1.000000e-200 139198.0 rs7254892 PVRL2 Q92692 R-HSA-418990 Adherens junctions interactions
300 LDL cholesterol -0.4853 0.0119 0.03166 1.000000e-200 139198.0 rs7254892 PVRL2 Q92692 R-HSA-198933 Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
300 LDL cholesterol -0.2209 0.0061 0.09763 1.000000e-200 170608.0 rs6511720 LDLR P01130 R-HSA-8964038 LDL clearance
300 LDL cholesterol -0.2209 0.0061 0.09763 1.000000e-200 170608.0 rs6511720 LDLR P01130 R-HSA-8964026 Chylomicron clearance
781 LDL cholesterol -0.5179 0.0146 0.03166 1.000000e-200 83075.7 rs7254892 TOMM40 O96008 R-HSA-1268020 Mitochondrial protein import
781 LDL cholesterol -0.5179 0.0146 0.03166 1.000000e-200 83075.7 rs7254892 PVRL2 Q92692 R-HSA-418990 Adherens junctions interactions
781 LDL cholesterol -0.5179 0.0146 0.03166 1.000000e-200 83075.7 rs7254892 PVRL2 Q92692 R-HSA-198933 Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
300 LDL cholesterol 0.1186 0.0040 0.28760 9.484185e-183 173007.0 rs1367117 APOB P04114 R-HSA-8866423 VLDL assembly
300 LDL cholesterol 0.1186 0.0040 0.28760 9.484185e-183 173007.0 rs1367117 APOB P04114 R-HSA-8963888 Chylomicron assembly
781 LDL cholesterol -0.2270 0.0082 0.09763 2.792544e-151 83042.9 rs6511720 LDLR P01130 R-HSA-8964038 LDL clearance
781 LDL cholesterol -0.2270 0.0082 0.09763 2.792544e-151 83042.9 rs6511720 LDLR P01130 R-HSA-8964026 Chylomicron clearance
300 LDL cholesterol -0.4970 0.0180 0.01715 8.570378e-143 77417.0 rs11591147 PCSK9 Q8NBP7 R-HSA-8964038 LDL clearance
300 LDL cholesterol -0.4970 0.0180 0.01715 8.570378e-143 77417.0 rs11591147 PCSK9 Q8NBP7 R-HSA-8866427 VLDLR internalisation and degradation
781 LDL cholesterol -0.4970 0.0180 0.01715 1.570363e-142 77417.0 rs11591147 PCSK9 Q8NBP7 R-HSA-8964038 LDL clearance
781 LDL cholesterol -0.4970 0.0180 0.01715 1.570363e-142 77417.0 rs11591147 PCSK9 Q8NBP7 R-HSA-8866427 VLDLR internalisation and degradation
300 LDL cholesterol -0.4462 0.0183 0.01715 2.992265e-122 99409.0 rs12721109 APOC2 P02655 R-HSA-8963889 Assembly of active LPL and LIPC lipase complexes
300 LDL cholesterol -0.4462 0.0183 0.01715 2.992265e-122 99409.0 rs12721109 APOC2 P02655 R-HSA-8964058 HDL remodeling
300 LDL cholesterol -0.4462 0.0183 0.01715 2.992265e-122 99409.0 rs12721109 APOC4 P55056 R-HSA-8866423 VLDL assembly
300 LDL cholesterol 0.0733 0.0038 0.43140 7.791122e-78 168357.0 rs12916 HMGCR P04035 R-HSA-1989781 PPARA activates gene expression
300 LDL cholesterol 0.0733 0.0038 0.43140 7.791122e-78 168357.0 rs12916 HMGCR P04035 R-HSA-2426168 Activation of gene expression by SREBF (SREBP)
781 LDL cholesterol -0.4413 0.0276 0.01715 1.310992e-53 34525.0 rs12721109 APOC2 P02655 R-HSA-8963889 Assembly of active LPL and LIPC lipase complexes
781 LDL cholesterol -0.4413 0.0276 0.01715 1.310992e-53 34525.0 rs12721109 APOC2 P02655 R-HSA-8964058 HDL remodeling
781 LDL cholesterol -0.4413 0.0276 0.01715 1.310992e-53 34525.0 rs12721109 APOC4 P55056 R-HSA-8866423 VLDL assembly
300 LDL cholesterol -0.1040 0.0072 0.07124 4.433023e-44 158643.0 rs2228603 NCAN O14594 R-HSA-3595177 Defective CHSY1 causes TPBS
300 LDL cholesterol -0.1040 0.0072 0.07124 4.433023e-44 158643.0 rs2228603 NCAN O14594 R-HSA-3560783 Defective B4GALT7 causes EDS,progeroid type
300 LDL cholesterol -0.1040 0.0072 0.07124 4.433023e-44 158643.0 rs2228603 NCAN O14594 R-HSA-4420332 Defective B3GALT6 causes EDSP2 and SEMDJL1
300 LDL cholesterol -0.1040 0.0072 0.07124 4.433023e-44 158643.0 rs2228603 NCAN O14594 R-HSA-3595172 Defective CHST3 causes SEDCJD
300 LDL cholesterol -0.1040 0.0072 0.07124 4.433023e-44 158643.0 rs2228603 NCAN O14594 R-HSA-3560801 Defective B3GAT3 causes JDSSDHD
300 LDL cholesterol -0.1040 0.0072 0.07124 4.433023e-44 158643.0 rs2228603 NCAN O14594 R-HSA-2022870 Chondroitin sulfate biosynthesis
300 LDL cholesterol -0.1040 0.0072 0.07124 4.433023e-44 158643.0 rs2228603 NCAN O14594 R-HSA-2024101 CS/DS degradation
300 LDL cholesterol -0.1040 0.0072 0.07124 4.433023e-44 158643.0 rs2228603 NCAN O14594 R-HSA-2022923 Dermatan sulfate biosynthesis
300 LDL cholesterol -0.1040 0.0072 0.07124 4.433023e-44 158643.0 rs2228603 NCAN O14594 R-HSA-1971475 A tetrasaccharide linker sequence is required for GAG synthesis
300 LDL cholesterol -0.1040 0.0072 0.07124 4.433023e-44 158643.0 rs2228603 NCAN O14594 R-HSA-419037 NCAM1 interactions
300 LDL cholesterol -0.1040 0.0072 0.07124 4.433023e-44 158643.0 rs2228603 NCAN O14594 R-HSA-373760 L1CAM interactions
781 LDL cholesterol 0.0687 0.0052 0.40900 3.394689e-35 83129.0 rs6453131 HMGCR P04035 R-HSA-1989781 PPARA activates gene expression
781 LDL cholesterol 0.0687 0.0052 0.40900 3.394689e-35 83129.0 rs6453131 HMGCR P04035 R-HSA-2426168 Activation of gene expression by SREBF (SREBP)
300 LDL cholesterol 0.0417 0.0036 0.46040 1.656151e-30 171333.0 rs6065311 TOP1 P11387 R-HSA-4615885 SUMOylation of DNA replication proteins
300 LDL cholesterol 0.1735 0.0161 0.02375 8.051930e-24 82003.8 rs75687619 TOMM40 O96008 R-HSA-1268020 Mitochondrial protein import
781 LDL cholesterol 0.1735 0.0161 0.02375 8.865434e-24 82003.8 rs75687619 TOMM40 O96008 R-HSA-1268020 Mitochondrial protein import
300 LDL cholesterol 0.0485 0.0049 0.19390 1.923092e-21 169889.0 rs2073547 NPC1L1 Q9UHC9 R-HSA-8963678 Intestinal lipid absorption
300 LDL cholesterol -0.0532 0.0058 0.44460 2.260997e-19 88433.0 rs2738459 LDLR P01130 R-HSA-8964038 LDL clearance
300 LDL cholesterol -0.0532 0.0058 0.44460 2.260997e-19 88433.0 rs2738459 LDLR P01130 R-HSA-8964026 Chylomicron clearance
300 LDL cholesterol -0.0382 0.0044 0.20980 2.086892e-17 172987.0 rs3757354 MYLIP Q8WY64 R-HSA-983168 Antigen processing: Ubiquitination & Proteasome degradation
300 LDL cholesterol 0.0339 0.0038 0.40500 2.671161e-17 164854.0 rs7832643 PLEC Q15149 R-HSA-446107 Type I hemidesmosome assembly
300 LDL cholesterol 0.0339 0.0038 0.40500 2.671161e-17 164854.0 rs7832643 PLEC Q15149 R-HSA-264870 Caspase-mediated cleavage of cytoskeletal proteins
300 LDL cholesterol -0.0302 0.0040 0.68210 7.490314e-14 172807.0 rs2419604 GPAM Q9HCL2 R-HSA-9018519 Estrogen-dependent gene expression
300 LDL cholesterol -0.0302 0.0040 0.68210 7.490314e-14 172807.0 rs2419604 GPAM Q9HCL2 R-HSA-8931987 RUNX1 regulates estrogen receptor mediated transcription
300 LDL cholesterol -0.0302 0.0040 0.68210 7.490314e-14 172807.0 rs2419604 GPAM Q9HCL2 R-HSA-2426168 Activation of gene expression by SREBF (SREBP)
781 LDL cholesterol 0.0391 0.0051 0.46040 1.856949e-13 83090.0 rs2223745 TOP1 P11387 R-HSA-4615885 SUMOylation of DNA replication proteins
781 LDL cholesterol 0.0475 0.0062 0.19390 5.645469e-13 83083.0 rs2073547 NPC1L1 Q9UHC9 R-HSA-8963678 Intestinal lipid absorption
781 LDL cholesterol 0.0472 0.0062 0.57120 8.421705e-13 57302.0 rs2738447 LDLR P01130 R-HSA-8964038 LDL clearance
781 LDL cholesterol 0.0472 0.0062 0.57120 8.421705e-13 57302.0 rs2738447 LDLR P01130 R-HSA-8964026 Chylomicron clearance
781 LDL cholesterol -0.0472 0.0063 0.77700 1.727030e-12 83094.0 rs3741298 APOA5 Q6Q788 R-HSA-8963889 Assembly of active LPL and LIPC lipase complexes
781 LDL cholesterol -0.0472 0.0063 0.77700 1.727030e-12 83094.0 rs3741298 APOA5 Q6Q788 R-HSA-1989781 PPARA activates gene expression
300 LDL cholesterol 0.0268 0.0038 0.53430 4.203393e-12 164996.0 rs3184504 SH2B3 Q9UQQ2 R-HSA-1433559 Regulation of KIT signaling
300 LDL cholesterol 0.0268 0.0038 0.53430 4.203393e-12 164996.0 rs3184504 SH2B3 Q9UQQ2 R-HSA-983231 Factors involved in megakaryocyte development and platelet production
300 LDL cholesterol 0.1028 0.0139 0.03694 9.808441e-12 111143.0 rs1801689 APOH P02749 R-HSA-114608 Platelet degranulation
300 LDL cholesterol -0.0243 0.0037 0.53830 2.260997e-11 171930.0 rs4942486 BRCA2 P51587 R-HSA-5693616 Presynaptic phase of homologous DNA pairing and strand exchange
300 LDL cholesterol -0.0243 0.0037 0.53830 2.260997e-11 171930.0 rs4942486 BRCA2 P51587 R-HSA-912446 Meiotic recombination
300 LDL cholesterol -0.0296 0.0044 0.24270 6.140447e-11 172330.0 rs1883025 ABCA1 O95477 R-HSA-1989781 PPARA activates gene expression
300 LDL cholesterol -0.0263 0.0037 0.39180 7.859592e-11 170097.0 rs6909746 FRK P42685 R-HSA-6798695 Neutrophil degranulation
300 LDL cholesterol -0.0263 0.0037 0.39180 7.859592e-11 170097.0 rs6909746 FRK P42685 R-HSA-8948751 Regulation of PTEN stability and activity
781 LDL cholesterol -0.0356 0.0052 0.61480 1.287004e-10 81819.0 rs6511727 DOCK6 Q96HP0 R-HSA-983231 Factors involved in megakaryocyte development and platelet production
300 LDL cholesterol -0.0242 0.0038 0.33510 3.435975e-10 169706.0 rs314253 DLG4 P78352 R-HSA-6794361 Neurexins and neuroligins
300 LDL cholesterol -0.0242 0.0038 0.33510 3.435975e-10 169706.0 rs314253 DLG4 P78352 R-HSA-8849932 Synaptic adhesion-like molecules
300 LDL cholesterol -0.0242 0.0038 0.33510 3.435975e-10 169706.0 rs314253 DLG4 P78352 R-HSA-447038 NrCAM interactions
300 LDL cholesterol -0.0242 0.0038 0.33510 3.435975e-10 169706.0 rs314253 DLG4 P78352 R-HSA-5625900 RHO GTPases activate CIT
781 LDL cholesterol -0.0334 0.0051 0.47360 5.991975e-10 83095.9 rs6920309 MYLIP Q8WY64 R-HSA-983168 Antigen processing: Ubiquitination & Proteasome degradation
300 LDL cholesterol -0.0685 0.0106 0.03430 6.034065e-10 142698.0 rs1800961 HNF4A P41235 R-HSA-383280 Nuclear Receptor transcription pathway
300 LDL cholesterol -0.0685 0.0106 0.03430 6.034065e-10 142698.0 rs1800961 HNF4A P41235 R-HSA-210745 Regulation of gene expression in beta cells
300 LDL cholesterol -0.0445 0.0074 0.05277 1.764006e-09 171976.0 rs3780181 VLDLR P98155 R-HSA-8866376 Reelin signalling pathway
300 LDL cholesterol -0.0445 0.0074 0.05277 1.764006e-09 171976.0 rs3780181 VLDLR P98155 R-HSA-8866427 VLDLR internalisation and degradation
300 LDL cholesterol -0.0445 0.0074 0.05277 1.764006e-09 171976.0 rs3780181 VLDLR P98155 R-HSA-8964046 VLDL clearance
300 LDL cholesterol -0.0336 0.0054 0.14380 1.832019e-09 172898.0 rs17404153 DNAJC13 O75165 R-HSA-6798695 Neutrophil degranulation
300 LDL cholesterol -0.0392 0.0069 0.10550 9.836939e-09 172228.0 rs7640978 CMTM6 Q9NX76 R-HSA-6798695 Neutrophil degranulation
781 LDL cholesterol -0.0327 0.0054 0.34040 1.296015e-08 83046.0 rs1175544 PPARG P37231 R-HSA-383280 Nuclear Receptor transcription pathway
781 LDL cholesterol -0.0327 0.0054 0.34040 1.296015e-08 83046.0 rs1175544 PPARG P37231 R-HSA-9022707 MECP2 regulates transcription factors
781 LDL cholesterol -0.0327 0.0054 0.34040 1.296015e-08 83046.0 rs1175544 PPARG P37231 R-HSA-381340 Transcriptional regulation of white adipocyte differentiation
781 LDL cholesterol -0.0327 0.0054 0.34040 1.296015e-08 83046.0 rs1175544 PPARG P37231 R-HSA-4090294 SUMOylation of intracellular receptors
300 LDL cholesterol 0.0243 0.0042 0.78890 3.129969e-08 173032.0 rs1250229 FN1 P02751 R-HSA-114608 Platelet degranulation
300 LDL cholesterol 0.0243 0.0042 0.78890 3.129969e-08 173032.0 rs1250229 FN1 P02751 R-HSA-354192 Integrin alphaIIb beta3 signaling
300 LDL cholesterol 0.0243 0.0042 0.78890 3.129969e-08 173032.0 rs1250229 FN1 P02751 R-HSA-6785807 Interleukin-4 and Interleukin-13 signaling
300 LDL cholesterol 0.0243 0.0042 0.78890 3.129969e-08 173032.0 rs1250229 FN1 P02751 R-HSA-216083 Integrin cell surface interactions
300 LDL cholesterol 0.0243 0.0042 0.78890 3.129969e-08 173032.0 rs1250229 FN1 P02751 R-HSA-1474244 Extracellular matrix organization
300 LDL cholesterol 0.0243 0.0042 0.78890 3.129969e-08 173032.0 rs1250229 FN1 P02751 R-HSA-1566977 Fibronectin matrix formation
300 LDL cholesterol 0.0311 0.0059 0.12400 3.352973e-08 171071.0 rs4253776 PPARA Q07869 R-HSA-383280 Nuclear Receptor transcription pathway
300 LDL cholesterol 0.0311 0.0059 0.12400 3.352973e-08 171071.0 rs4253776 PPARA Q07869 R-HSA-1368108 BMAL1:CLOCK,NPAS2 activates circadian gene expression
300 LDL cholesterol 0.0311 0.0059 0.12400 3.352973e-08 171071.0 rs4253776 PPARA Q07869 R-HSA-400206 Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)
300 LDL cholesterol 0.0311 0.0059 0.12400 3.352973e-08 171071.0 rs4253776 PPARA Q07869 R-HSA-1989781 PPARA activates gene expression
300 LDL cholesterol 0.0311 0.0059 0.12400 3.352973e-08 171071.0 rs4253776 PPARA Q07869 R-HSA-4090294 SUMOylation of intracellular receptors
300 LDL cholesterol 0.0345 0.0062 0.12530 4.499042e-08 172855.0 rs11563251 UGT1A9 O60656 R-HSA-1989781 PPARA activates gene expression
781 LDL cholesterol 0.0300 0.0052 0.40500 4.858028e-08 82044.0 rs7832643 PLEC Q15149 R-HSA-446107 Type I hemidesmosome assembly
781 LDL cholesterol 0.0300 0.0052 0.40500 4.858028e-08 82044.0 rs7832643 PLEC Q15149 R-HSA-264870 Caspase-mediated cleavage of cytoskeletal proteins
MATCH (gwas:Gwas {trait: "LDL cholesterol"}) <-[mre_study_snp:MRE_STUDY_SNP]-(snp:Snp)-[snp_gene:SNP_GENE]-> (gene:Gene)-[gene_to_protein:GENE_TO_PROTEIN]->(protein:Protein) -[protein_in_pathway:PROTEIN_IN_PATHWAY]->(pathway:Pathway) WHERE mre_study_snp.pval < 1e-05 AND snp.name is not null AND gene.name is not null RETURN gwas {.id, .trait}, mre_study_snp {.se, .eaf, .pval, .samplesize, .beta}, snp {.name}, gene {.name}, protein {.uniprot_id}, pathway {.reactome_id, .name} ORDER BY mre_study_snp.pval ;
curl -X 'GET' -H 'Accept: */*' -H 'Accept-Encoding: gzip, deflate' -H 'Connection: keep-alive' -H 'User-Agent: python-requests/2.22.0' 'http://api.epigraphdb.org_private/pathway?trait_name=LDL+cholesterol&pval_threshold=1e-05'