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 the top 150 relationships

 

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
12 Crohn's disease -0.335814 0.012476 0.435200 1.377209e-159 51874.0 rs7517847 IL23R Q5VWK5 R-HSA-6785807 Interleukin-4 and Interleukin-13 signaling
12 Crohn's disease -0.335814 0.012476 0.435200 1.377209e-159 51874.0 rs7517847 IL23R Q5VWK5 R-HSA-9020933 Interleukin-23 signaling
12 Crohn's disease 0.226164 0.012089 0.527400 4.257945e-78 51874.0 rs6738490 ATG16L1 Q676U5 R-HSA-1632852 Macroautophagy
30 Crohn's disease 0.399806 0.024200 0.283672 3.244890e-61 20883.0 rs2076756 NOD2 Q9HC29 R-HSA-168638 NOD1/2 Signaling Pathway
30 Crohn's disease -0.995199 0.063900 0.056321 1.051962e-54 20883.0 rs11209026 IL23R Q5VWK5 R-HSA-6785807 Interleukin-4 and Interleukin-13 signaling
30 Crohn's disease -0.995199 0.063900 0.056321 1.051962e-54 20883.0 rs11209026 IL23R Q5VWK5 R-HSA-9020933 Interleukin-23 signaling
11 Crohn's disease 0.642073 0.045461 0.601000 2.519997e-45 5409.0 rs4366152 TNFSF15 O95150 R-HSA-5669034 TNFs bind their physiological receptors
30 Crohn's disease 0.301402 0.023200 0.543391 1.859945e-38 20883.0 rs12692254 ATG16L1 Q676U5 R-HSA-1632852 Macroautophagy
12 Crohn's disease 0.155114 0.012878 0.281200 2.052107e-33 51874.0 rs3197999 MST1 P26927 R-HSA-8852405 Signaling by MST1
12 Crohn's disease 0.150794 0.012830 0.352900 6.777976e-32 51874.0 rs9264942 HLA-B P30486 R-HSA-909733 Interferon alpha/beta signaling
12 Crohn's disease 0.150794 0.012830 0.352900 6.777976e-32 51874.0 rs9264942 HLA-B P30486 R-HSA-877300 Interferon gamma signaling
12 Crohn's disease 0.150794 0.012830 0.352900 6.777976e-32 51874.0 rs9264942 HLA-B Q29836 R-HSA-909733 Interferon alpha/beta signaling
12 Crohn's disease 0.150794 0.012830 0.352900 6.777976e-32 51874.0 rs9264942 HLA-B Q29836 R-HSA-877300 Interferon gamma signaling
12 Crohn's disease 0.150794 0.012830 0.352900 6.777976e-32 51874.0 rs9264942 HLA-B Q31610 R-HSA-877300 Interferon gamma signaling
12 Crohn's disease 0.150794 0.012830 0.352900 6.777976e-32 51874.0 rs9264942 HLA-B Q31610 R-HSA-909733 Interferon alpha/beta signaling
12 Crohn's disease 0.150794 0.012830 0.352900 6.777976e-32 51874.0 rs9264942 HLA-B P01889 R-HSA-909733 Interferon alpha/beta signaling
12 Crohn's disease 0.150794 0.012830 0.352900 6.777976e-32 51874.0 rs9264942 HLA-B P01889 R-HSA-877300 Interferon gamma signaling
12 Crohn's disease 0.150794 0.012830 0.352900 6.777976e-32 51874.0 rs9264942 HLA-B P01889 R-HSA-6798695 Neutrophil degranulation
12 Crohn's disease 0.150794 0.012830 0.352900 6.777976e-32 51874.0 rs9264942 HLA-B P30480 R-HSA-877300 Interferon gamma signaling
12 Crohn's disease 0.150794 0.012830 0.352900 6.777976e-32 51874.0 rs9264942 HLA-B P30480 R-HSA-909733 Interferon alpha/beta signaling
12 Crohn's disease 0.150794 0.012830 0.352900 6.777976e-32 51874.0 rs9264942 HLA-B Q31612 R-HSA-909733 Interferon alpha/beta signaling
12 Crohn's disease 0.150794 0.012830 0.352900 6.777976e-32 51874.0 rs9264942 HLA-B Q31612 R-HSA-877300 Interferon gamma signaling
12 Crohn's disease 0.394341 0.037028 0.018830 1.747029e-26 51874.0 rs76906269 LRRK2 Q5S007 R-HSA-8857538 PTK6 promotes HIF1A stabilization
12 Crohn's disease 0.133849 0.012855 0.319500 2.179215e-25 51874.0 rs11152949 PRDM1 O75626 R-HSA-6804754 Regulation of TP53 Expression
12 Crohn's disease 0.119845 0.012247 0.457600 1.293302e-22 51874.0 rs26528 IL27 Q8NEV9 R-HSA-9020956 Interleukin-27 signaling
12 Crohn's disease -0.122687 0.012571 0.375700 1.676872e-22 51874.0 rs13001325 IL18R1 Q13478 R-HSA-9012546 Interleukin-18 signaling
12 Crohn's disease -0.122687 0.012571 0.375700 1.676872e-22 51874.0 rs13001325 IL18R1 Q13478 R-HSA-9008059 Interleukin-37 signaling
12 Crohn's disease -0.122687 0.012571 0.375700 1.676872e-22 51874.0 rs13001325 IL1RL1 Q01638 R-HSA-9014843 Interleukin-33 signaling
12 Crohn's disease 0.120078 0.012410 0.569400 3.815926e-22 51874.0 rs6062496 TNFRSF6B O95407 R-HSA-5669034 TNFs bind their physiological receptors
12 Crohn's disease -0.116483 0.012061 0.605100 4.557220e-22 51874.0 rs780094 GCKR Q14397 R-HSA-170822 Regulation of Glucokinase by Glucokinase Regul...
12 Crohn's disease 0.159076 0.017281 0.132200 3.415073e-20 51874.0 rs438475 NOTCH4 Q99466 R-HSA-350054 Notch-HLH transcription pathway
12 Crohn's disease 0.159076 0.017281 0.132200 3.415073e-20 51874.0 rs438475 NOTCH4 Q99466 R-HSA-1912399 Pre-NOTCH Processing in the Endoplasmic Reticulum
12 Crohn's disease 0.159076 0.017281 0.132200 3.415073e-20 51874.0 rs438475 NOTCH4 Q99466 R-HSA-9013700 NOTCH4 Activation and Transmission of Signal t...
12 Crohn's disease 0.159076 0.017281 0.132200 3.415073e-20 51874.0 rs438475 NOTCH4 Q99466 R-HSA-9013695 NOTCH4 Intracellular Domain Regulates Transcri...
12 Crohn's disease 0.159076 0.017281 0.132200 3.415073e-20 51874.0 rs438475 NOTCH4 Q99466 R-HSA-9604323 Negative regulation of NOTCH4 signaling
12 Crohn's disease 0.159076 0.017281 0.132200 3.415073e-20 51874.0 rs438475 NOTCH4 Q99466 R-HSA-1912408 Pre-NOTCH Transcription and Translation
12 Crohn's disease 0.128384 0.013960 0.236400 3.698282e-20 51874.0 rs17293632 SMAD3 P84022 R-HSA-3311021 SMAD4 MH2 Domain Mutants in Cancer
12 Crohn's disease 0.128384 0.013960 0.236400 3.698282e-20 51874.0 rs17293632 SMAD3 P84022 R-HSA-3656532 TGFBR1 KD Mutants in Cancer
12 Crohn's disease 0.128384 0.013960 0.236400 3.698282e-20 51874.0 rs17293632 SMAD3 P84022 R-HSA-1181150 Signaling by NODAL
12 Crohn's disease 0.128384 0.013960 0.236400 3.698282e-20 51874.0 rs17293632 SMAD3 P84022 R-HSA-2173795 Downregulation of SMAD2/3:SMAD4 transcriptiona...
12 Crohn's disease 0.128384 0.013960 0.236400 3.698282e-20 51874.0 rs17293632 SMAD3 P84022 R-HSA-2173788 Downregulation of TGF-beta receptor signaling
12 Crohn's disease 0.128384 0.013960 0.236400 3.698282e-20 51874.0 rs17293632 SMAD3 P84022 R-HSA-2173789 TGF-beta receptor signaling activates SMADs
12 Crohn's disease 0.128384 0.013960 0.236400 3.698282e-20 51874.0 rs17293632 SMAD3 P84022 R-HSA-2173796 SMAD2/SMAD3:SMAD4 heterotrimer regulates trans...
12 Crohn's disease 0.128384 0.013960 0.236400 3.698282e-20 51874.0 rs17293632 SMAD3 P84022 R-HSA-1502540 Signaling by Activin
12 Crohn's disease 0.128384 0.013960 0.236400 3.698282e-20 51874.0 rs17293632 SMAD3 P84022 R-HSA-9008059 Interleukin-37 signaling
12 Crohn's disease 0.128384 0.013960 0.236400 3.698282e-20 51874.0 rs17293632 SMAD3 P84022 R-HSA-9013695 NOTCH4 Intracellular Domain Regulates Transcri...
30 Crohn's disease 0.215901 0.023500 0.419834 4.370187e-20 20883.0 rs4077515 CARD9 Q9H257 R-HSA-5607764 CLEC7A (Dectin-1) signaling
30 Crohn's disease 0.215901 0.023500 0.419834 4.370187e-20 20883.0 rs4077515 CARD9 Q9H257 R-HSA-168638 NOD1/2 Signaling Pathway
12 Crohn's disease -0.104177 0.012359 0.418500 3.473762e-17 51874.0 rs12949918 STAT3 P40763 R-HSA-2586552 Signaling by Leptin
12 Crohn's disease -0.104177 0.012359 0.418500 3.473762e-17 51874.0 rs12949918 STAT3 P40763 R-HSA-8984722 Interleukin-35 Signalling
12 Crohn's disease -0.104177 0.012359 0.418500 3.473762e-17 51874.0 rs12949918 STAT3 P40763 R-HSA-9020933 Interleukin-23 signaling
12 Crohn's disease -0.104177 0.012359 0.418500 3.473762e-17 51874.0 rs12949918 STAT3 P40763 R-HSA-9020956 Interleukin-27 signaling
12 Crohn's disease -0.104177 0.012359 0.418500 3.473762e-17 51874.0 rs12949918 STAT3 P40763 R-HSA-6783783 Interleukin-10 signaling
12 Crohn's disease -0.104177 0.012359 0.418500 3.473762e-17 51874.0 rs12949918 STAT3 P40763 R-HSA-1266695 Interleukin-7 signaling
12 Crohn's disease -0.104177 0.012359 0.418500 3.473762e-17 51874.0 rs12949918 STAT3 P40763 R-HSA-2892247 POU5F1 (OCT4),SOX2,NANOG activate genes relate...
12 Crohn's disease -0.104177 0.012359 0.418500 3.473762e-17 51874.0 rs12949918 STAT3 P40763 R-HSA-186763 Downstream signal transduction
12 Crohn's disease -0.104177 0.012359 0.418500 3.473762e-17 51874.0 rs12949918 STAT3 P40763 R-HSA-1433557 Signaling by SCF-KIT
12 Crohn's disease -0.104177 0.012359 0.418500 3.473762e-17 51874.0 rs12949918 STAT3 P40763 R-HSA-1839117 Signaling by cytosolic FGFR1 fusion mutants
12 Crohn's disease -0.104177 0.012359 0.418500 3.473762e-17 51874.0 rs12949918 STAT3 P40763 R-HSA-8983432 Interleukin-15 signaling
12 Crohn's disease -0.104177 0.012359 0.418500 3.473762e-17 51874.0 rs12949918 STAT3 P40763 R-HSA-9020958 Interleukin-21 signaling
12 Crohn's disease -0.104177 0.012359 0.418500 3.473762e-17 51874.0 rs12949918 STAT3 P40763 R-HSA-8985947 Interleukin-9 signaling
12 Crohn's disease -0.104177 0.012359 0.418500 3.473762e-17 51874.0 rs12949918 STAT3 P40763 R-HSA-1059683 Interleukin-6 signaling
12 Crohn's disease -0.104177 0.012359 0.418500 3.473762e-17 51874.0 rs12949918 STAT3 P40763 R-HSA-390471 Association of TriC/CCT with target proteins d...
12 Crohn's disease -0.104177 0.012359 0.418500 3.473762e-17 51874.0 rs12949918 STAT3 P40763 R-HSA-982772 Growth hormone receptor signaling
12 Crohn's disease -0.104177 0.012359 0.418500 3.473762e-17 51874.0 rs12949918 STAT3 P40763 R-HSA-6785807 Interleukin-4 and Interleukin-13 signaling
12 Crohn's disease -0.104177 0.012359 0.418500 3.473762e-17 51874.0 rs12949918 STAT3 P40763 R-HSA-8854691 Interleukin-20 family signaling
12 Crohn's disease -0.104177 0.012359 0.418500 3.473762e-17 51874.0 rs12949918 STAT3 P40763 R-HSA-8849474 PTK6 Activates STAT3
12 Crohn's disease -0.104177 0.012359 0.418500 3.473762e-17 51874.0 rs12949918 STAT3 P40763 R-HSA-198745 Signalling to STAT3
12 Crohn's disease -0.104177 0.012359 0.418500 3.473762e-17 51874.0 rs12949918 STAT3 P40763 R-HSA-9008059 Interleukin-37 signaling
12 Crohn's disease -0.104177 0.012359 0.418500 3.473762e-17 51874.0 rs12949918 STAT3 P40763 R-HSA-8875791 MET activates STAT3
30 Crohn's disease 0.283102 0.035300 0.112701 1.081932e-15 20883.0 rs80262450 PTPN2 P17706 R-HSA-9008059 Interleukin-37 signaling
30 Crohn's disease 0.207799 0.026300 0.698408 2.462068e-15 20883.0 rs3810936 TNFSF15 O95150 R-HSA-5669034 TNFs bind their physiological receptors
12 Crohn's disease 0.105079 0.014020 0.233700 6.632847e-14 51874.0 rs3801810 SKAP2 O75563 R-HSA-391160 Signal regulatory protein family interactions
12 Crohn's disease 0.155227 0.020760 0.086810 7.592766e-14 51874.0 rs11159833 GPR65 Q8IYL9 R-HSA-373076 Class A/1 (Rhodopsin-like receptors)
12 Crohn's disease 0.148159 0.020335 0.089830 3.192273e-13 51874.0 rs61839660 IL2RA P01589 R-HSA-9020558 Interleukin-2 signaling
12 Crohn's disease 0.148159 0.020335 0.089830 3.192273e-13 51874.0 rs61839660 IL2RA P01589 R-HSA-8877330 RUNX1 and FOXP3 control the development of reg...
12 Crohn's disease 0.099446 0.013749 0.728800 4.723892e-13 51874.0 rs2227551 PLAU P00749 R-HSA-6798695 Neutrophil degranulation
12 Crohn's disease 0.099446 0.013749 0.728800 4.723892e-13 51874.0 rs2227551 PLAU P00749 R-HSA-75205 Dissolution of Fibrin Clot
30 Crohn's disease 0.193097 0.026900 0.234271 7.452466e-13 20883.0 rs56062135 SMAD3 P84022 R-HSA-3311021 SMAD4 MH2 Domain Mutants in Cancer
30 Crohn's disease 0.193097 0.026900 0.234271 7.452466e-13 20883.0 rs56062135 SMAD3 P84022 R-HSA-3656532 TGFBR1 KD Mutants in Cancer
30 Crohn's disease 0.193097 0.026900 0.234271 7.452466e-13 20883.0 rs56062135 SMAD3 P84022 R-HSA-1181150 Signaling by NODAL
30 Crohn's disease 0.193097 0.026900 0.234271 7.452466e-13 20883.0 rs56062135 SMAD3 P84022 R-HSA-2173795 Downregulation of SMAD2/3:SMAD4 transcriptiona...
30 Crohn's disease 0.193097 0.026900 0.234271 7.452466e-13 20883.0 rs56062135 SMAD3 P84022 R-HSA-2173788 Downregulation of TGF-beta receptor signaling
30 Crohn's disease 0.193097 0.026900 0.234271 7.452466e-13 20883.0 rs56062135 SMAD3 P84022 R-HSA-2173789 TGF-beta receptor signaling activates SMADs
30 Crohn's disease 0.193097 0.026900 0.234271 7.452466e-13 20883.0 rs56062135 SMAD3 P84022 R-HSA-2173796 SMAD2/SMAD3:SMAD4 heterotrimer regulates trans...
30 Crohn's disease 0.193097 0.026900 0.234271 7.452466e-13 20883.0 rs56062135 SMAD3 P84022 R-HSA-1502540 Signaling by Activin
30 Crohn's disease 0.193097 0.026900 0.234271 7.452466e-13 20883.0 rs56062135 SMAD3 P84022 R-HSA-9008059 Interleukin-37 signaling
30 Crohn's disease 0.193097 0.026900 0.234271 7.452466e-13 20883.0 rs56062135 SMAD3 P84022 R-HSA-9013695 NOTCH4 Intracellular Domain Regulates Transcri...
30 Crohn's disease -0.168099 0.024300 0.623303 4.223767e-12 20883.0 rs1887428 JAK2 O60674 R-HSA-6788467 IL-6-type cytokine receptor ligand interactions
30 Crohn's disease -0.168099 0.024300 0.623303 4.223767e-12 20883.0 rs1887428 JAK2 O60674 R-HSA-1059683 Interleukin-6 signaling
30 Crohn's disease -0.168099 0.024300 0.623303 4.223767e-12 20883.0 rs1887428 JAK2 O60674 R-HSA-9020956 Interleukin-27 signaling
30 Crohn's disease -0.168099 0.024300 0.623303 4.223767e-12 20883.0 rs1887428 JAK2 O60674 R-HSA-1433557 Signaling by SCF-KIT
30 Crohn's disease -0.168099 0.024300 0.623303 4.223767e-12 20883.0 rs1887428 JAK2 O60674 R-HSA-512988 Interleukin-3,Interleukin-5 and GM-CSF signaling
30 Crohn's disease -0.168099 0.024300 0.623303 4.223767e-12 20883.0 rs1887428 JAK2 O60674 R-HSA-1170546 Prolactin receptor signaling
30 Crohn's disease -0.168099 0.024300 0.623303 4.223767e-12 20883.0 rs1887428 JAK2 O60674 R-HSA-982772 Growth hormone receptor signaling
30 Crohn's disease -0.168099 0.024300 0.623303 4.223767e-12 20883.0 rs1887428 JAK2 O60674 R-HSA-983231 Factors involved in megakaryocyte development ...
30 Crohn's disease -0.168099 0.024300 0.623303 4.223767e-12 20883.0 rs1887428 JAK2 O60674 R-HSA-6785807 Interleukin-4 and Interleukin-13 signaling
30 Crohn's disease -0.168099 0.024300 0.623303 4.223767e-12 20883.0 rs1887428 JAK2 O60674 R-HSA-9020591 Interleukin-12 signaling
30 Crohn's disease -0.168099 0.024300 0.623303 4.223767e-12 20883.0 rs1887428 JAK2 O60674 R-HSA-9020933 Interleukin-23 signaling
12 Crohn's disease 0.103233 0.014966 0.200700 5.282019e-12 51874.0 rs72727394 RASGRP1 O95267 R-HSA-1169092 Activation of RAS in B cells
12 Crohn's disease 0.103233 0.014966 0.200700 5.282019e-12 51874.0 rs72727394 RASGRP1 O95267 R-HSA-2871837 FCERI mediated NF-kB activation
12 Crohn's disease 0.103233 0.014966 0.200700 5.282019e-12 51874.0 rs72727394 RASGRP1 O95267 R-HSA-114508 Effects of PIP2 hydrolysis
12 Crohn's disease 0.085659 0.012654 0.438700 1.293302e-11 51874.0 rs28999107 LTBR P36941 R-HSA-5676594 TNF receptor superfamily (TNFSF) members media...
12 Crohn's disease -0.156770 0.023765 0.071450 4.204361e-11 51874.0 rs10878302 LRRK2 Q5S007 R-HSA-8857538 PTK6 promotes HIF1A stabilization
30 Crohn's disease -0.168899 0.026100 0.759729 9.935735e-11 20883.0 rs4851586 IL18RAP O95256 R-HSA-9012546 Interleukin-18 signaling
12 Crohn's disease 0.080010 0.012452 0.604800 1.313621e-10 51874.0 rs1517352 STAT4 Q14765 R-HSA-9020958 Interleukin-21 signaling
12 Crohn's disease 0.080010 0.012452 0.604800 1.313621e-10 51874.0 rs1517352 STAT4 Q14765 R-HSA-8854691 Interleukin-20 family signaling
12 Crohn's disease 0.080010 0.012452 0.604800 1.313621e-10 51874.0 rs1517352 STAT4 Q14765 R-HSA-9020591 Interleukin-12 signaling
12 Crohn's disease 0.080010 0.012452 0.604800 1.313621e-10 51874.0 rs1517352 STAT4 Q14765 R-HSA-8984722 Interleukin-35 Signalling
12 Crohn's disease 0.080010 0.012452 0.604800 1.313621e-10 51874.0 rs1517352 STAT4 Q14765 R-HSA-9020933 Interleukin-23 signaling
30 Crohn's disease 0.154901 0.024400 0.369415 2.335985e-10 20883.0 rs147684209 SH2B1 Q9NRF2 R-HSA-2586552 Signaling by Leptin
30 Crohn's disease 0.154901 0.024400 0.369415 2.335985e-10 20883.0 rs147684209 SH2B1 Q9NRF2 R-HSA-1170546 Prolactin receptor signaling
30 Crohn's disease 0.154901 0.024400 0.369415 2.335985e-10 20883.0 rs147684209 SH2B1 Q9NRF2 R-HSA-983231 Factors involved in megakaryocyte development ...
30 Crohn's disease 0.173996 0.028600 0.199556 1.166998e-09 20883.0 rs8137950 UBE2L3 P68036 R-HSA-8866652 Synthesis of active ubiquitin: roles of E1 and...
30 Crohn's disease 0.173996 0.028600 0.199556 1.166998e-09 20883.0 rs8137950 UBE2L3 P68036 R-HSA-8866654 E3 ubiquitin ligases ubiquitinate target proteins
30 Crohn's disease 0.224303 0.037300 0.116563 1.851015e-09 20883.0 rs28701841 PRDM1 O75626 R-HSA-6804754 Regulation of TP53 Expression
30 Crohn's disease 0.224303 0.037300 0.116563 1.851015e-09 20883.0 rs28701841 ATG5 Q9H1Y0 R-HSA-1632852 Macroautophagy
12 Crohn's disease -0.070387 0.011982 0.492500 4.247173e-09 51874.0 rs10798069 PLA2G4A P47712 R-HSA-111995 phospho-PLA2 pathway
12 Crohn's disease -0.070387 0.011982 0.492500 4.247173e-09 51874.0 rs10798069 PLA2G4A P47712 R-HSA-418592 ADP signalling through P2Y purinoceptor 1
12 Crohn's disease -0.070387 0.011982 0.492500 4.247173e-09 51874.0 rs10798069 PLA2G4A P47712 R-HSA-432142 Platelet sensitization by LDL
11 Crohn's disease -0.329049 0.056935 0.188200 7.460020e-09 5409.0 rs16894919 OR11A1 Q9GZK7 R-HSA-381753 Olfactory Signaling Pathway
12 Crohn's disease -0.099661 0.017342 0.153700 9.094525e-09 51874.0 rs7236492 NFATC1 O95644 R-HSA-2871809 FCERI mediated Ca+2 mobilization
12 Crohn's disease -0.099661 0.017342 0.153700 9.094525e-09 51874.0 rs7236492 NFATC1 O95644 R-HSA-5607763 CLEC7A (Dectin-1) induces NFAT activation
12 Crohn's disease -0.099661 0.017342 0.153700 9.094525e-09 51874.0 rs7236492 NFATC1 O95644 R-HSA-2025928 Calcineurin activates NFAT
12 Crohn's disease -0.099661 0.017342 0.153700 9.094525e-09 51874.0 rs7236492 NFATC1 O95644 R-HSA-4086398 Ca2+ pathway
11 Crohn's disease 0.235293 0.041510 0.531500 1.439992e-08 5409.0 rs9368758 COL11A2 P13942 R-HSA-8948216 Collagen chain trimerization
12 Crohn's disease -0.067651 0.011997 0.507400 1.710173e-08 51874.0 rs3184504 SH2B3 Q9UQQ2 R-HSA-1433559 Regulation of KIT signaling
12 Crohn's disease -0.067651 0.011997 0.507400 1.710173e-08 51874.0 rs3184504 SH2B3 Q9UQQ2 R-HSA-983231 Factors involved in megakaryocyte development ...
30 Crohn's disease -0.129299 0.023300 0.408159 2.923008e-08 20883.0 rs744166 STAT3 P40763 R-HSA-2586552 Signaling by Leptin
30 Crohn's disease -0.129299 0.023300 0.408159 2.923008e-08 20883.0 rs744166 STAT3 P40763 R-HSA-8984722 Interleukin-35 Signalling
30 Crohn's disease -0.129299 0.023300 0.408159 2.923008e-08 20883.0 rs744166 STAT3 P40763 R-HSA-9020933 Interleukin-23 signaling
30 Crohn's disease -0.129299 0.023300 0.408159 2.923008e-08 20883.0 rs744166 STAT3 P40763 R-HSA-9020956 Interleukin-27 signaling
30 Crohn's disease -0.129299 0.023300 0.408159 2.923008e-08 20883.0 rs744166 STAT3 P40763 R-HSA-6783783 Interleukin-10 signaling
30 Crohn's disease -0.129299 0.023300 0.408159 2.923008e-08 20883.0 rs744166 STAT3 P40763 R-HSA-1266695 Interleukin-7 signaling
30 Crohn's disease -0.129299 0.023300 0.408159 2.923008e-08 20883.0 rs744166 STAT3 P40763 R-HSA-2892247 POU5F1 (OCT4),SOX2,NANOG activate genes relate...
30 Crohn's disease -0.129299 0.023300 0.408159 2.923008e-08 20883.0 rs744166 STAT3 P40763 R-HSA-186763 Downstream signal transduction
30 Crohn's disease -0.129299 0.023300 0.408159 2.923008e-08 20883.0 rs744166 STAT3 P40763 R-HSA-1433557 Signaling by SCF-KIT
30 Crohn's disease -0.129299 0.023300 0.408159 2.923008e-08 20883.0 rs744166 STAT3 P40763 R-HSA-1839117 Signaling by cytosolic FGFR1 fusion mutants
30 Crohn's disease -0.129299 0.023300 0.408159 2.923008e-08 20883.0 rs744166 STAT3 P40763 R-HSA-8983432 Interleukin-15 signaling
30 Crohn's disease -0.129299 0.023300 0.408159 2.923008e-08 20883.0 rs744166 STAT3 P40763 R-HSA-9020958 Interleukin-21 signaling
30 Crohn's disease -0.129299 0.023300 0.408159 2.923008e-08 20883.0 rs744166 STAT3 P40763 R-HSA-8985947 Interleukin-9 signaling
30 Crohn's disease -0.129299 0.023300 0.408159 2.923008e-08 20883.0 rs744166 STAT3 P40763 R-HSA-1059683 Interleukin-6 signaling
30 Crohn's disease -0.129299 0.023300 0.408159 2.923008e-08 20883.0 rs744166 STAT3 P40763 R-HSA-390471 Association of TriC/CCT with target proteins d...
30 Crohn's disease -0.129299 0.023300 0.408159 2.923008e-08 20883.0 rs744166 STAT3 P40763 R-HSA-982772 Growth hormone receptor signaling
30 Crohn's disease -0.129299 0.023300 0.408159 2.923008e-08 20883.0 rs744166 STAT3 P40763 R-HSA-6785807 Interleukin-4 and Interleukin-13 signaling
30 Crohn's disease -0.129299 0.023300 0.408159 2.923008e-08 20883.0 rs744166 STAT3 P40763 R-HSA-8854691 Interleukin-20 family signaling
30 Crohn's disease -0.129299 0.023300 0.408159 2.923008e-08 20883.0 rs744166 STAT3 P40763 R-HSA-8849474 PTK6 Activates STAT3
30 Crohn's disease -0.129299 0.023300 0.408159 2.923008e-08 20883.0 rs744166 STAT3 P40763 R-HSA-198745 Signalling to STAT3
30 Crohn's disease -0.129299 0.023300 0.408159 2.923008e-08 20883.0 rs744166 STAT3 P40763 R-HSA-9008059 Interleukin-37 signaling
30 Crohn's disease -0.129299 0.023300 0.408159 2.923008e-08 20883.0 rs744166 STAT3 P40763 R-HSA-8875791 MET activates STAT3
11 Crohn's disease -0.245064 0.044844 0.729600 4.629989e-08 5409.0 rs2975785 GPR35 Q9HC97 R-HSA-373076 Class A/1 (Rhodopsin-like receptors)

Query diagram

Cypher query

MATCH (gwas:Gwas {trait: "Crohn's disease"}) <-[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 ;

API call

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/pathway?trait_name=Crohn%27s+disease&pval_threshold=1e-05'

Response data

{
    "query": "MATCH (gwas:Gwas {trait: \"Crohn's disease\"}) <-[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 ;",
    "results": [
        {
            "gwas": {
                "trait": "Crohn's disease",
                "id": "12"
            },
            "mre_study_snp": {
                "se": 0.0124758,
                "eaf": 0.4352,
                "pval": 1.37720946889398e-159,
                "samplesize": 51874.0,
                "beta": -0.335814
            },
            "snp": {
                "name": "rs7517847"
            },
            "gene": {
                "name": "IL23R"
            },
            "protein": {
                "uniprot_id": "Q5VWK5"
            },
            "pathway": {
                "name": "Interleukin-4 and Interleukin-13 signaling",
                "reactome_id": "R-HSA-6785807"
            }
        },
        {
            "gwas": {
                "trait": "Crohn's disease",
                "id": "12"
            },
            "mre_study_snp": {
                "se": 0.0124758,
                "eaf": 0.4352,
                "pval": 1.37720946889398e-159,
                "samplesize": 51874.0,
                "beta": -0.335814
            },
            "snp": {
                "name": "rs7517847"
            },
            "gene": {
                "name": "IL23R"
            },
            "protein": {
                "uniprot_id": "Q5VWK5"
            },
            "pathway": {
                "name": "Interleukin-23 signaling",
                "reactome_id": "R-HSA-9020933"
            }
        },
        {
            "gwas": {
                "trait": "Crohn's disease",
                "id": "12"
            },
            "mre_study_snp": {
                "se": 0.0120892,
                "eaf": 0.5274,
                "pval": 4.25794453582594e-78,
                "samplesize": 51874.0,
                "beta": 0.226164
            },
            "snp": {
                "name": "rs6738490"
            },
            "gene": {
                "name": "ATG16L1"
            },
            "protein": {
                "uniprot_id": "Q676U5"
            },
            "pathway": {
                "name": "Macroautophagy",
                "reactome_id": "R-HSA-1632852"
            }
        },
        {
            "gwas": {
                "trait": "Crohn's disease",
                "id": "30"
            },
            "mre_study_snp": {
                "se": 0.0242,
                "eaf": 0.283672,
                "pval": 3.24489015660538e-61,
                "samplesize": 20883.0,
                "beta": 0.399806
            },
            "snp": {
                "name": "rs2076756"
            },
            "gene": {
                "name": "NOD2"
            },
            "protein": {
                "uniprot_id": "Q9HC29"
            },
            "pathway": {
                "name": "NOD1/2 Signaling Pathway",
                "reactome_id": "R-HSA-168638"
            }
        },
        {
            "gwas": {
                "trait": "Crohn's disease",
                "id": "30"
            },
            "mre_study_snp": {
                "se": 0.0639,
                "eaf": 0.0563213,
                "pval": 1.05196187382322e-54,
                "samplesize": 20883.0,
                "beta": -0.995199
            },
            "snp": {
                "name": "rs11209026"
            },
            "gene": {
                "name": "IL23R"
            },
            "protein": {
                "uniprot_id": "Q5VWK5"
            },
            "pathway": {
                "name": "Interleukin-4 and Interleukin-13 signaling",
                "reactome_id": "R-HSA-6785807"
            }
        },
        {
            "gwas": {
                "trait": "Crohn's disease",
                "id": "30"
            },
            "mre_study_snp": {
                "se": 0.0639,
                "eaf": 0.0563213,
                "pval": 1.05196187382322e-54,
                "samplesize": 20883.0,
                "beta": -0.995199
            },
            "snp": {
                "name": "rs11209026"
            },
            "gene": {
                "name": "IL23R"
            },
            "protein": {
                "uniprot_id": "Q5VWK5"
            },
            "pathway": {
                "name": "Interleukin-23 signaling",
                "reactome_id": "R-HSA-9020933"
            }
        },
        {
            "gwas": {
                "trait": "Crohn's disease",
                "id": "11"
            },
            "mre_study_snp": {
                "se": 0.0454612,
                "eaf": 0.601,
                "pval": 2.51999686210925e-45,
                "samplesize": 5409.0,
                "beta": 0.642073
            },
            "snp": {
                "name": "rs4366152"
            },
            "gene": {
                "name": "TNFSF15"
            },
            "protein": {
                "uniprot_id": "O95150"
            },
            "pathway": {
                "name": "TNFs bind their physiological receptors",
                "reactome_id": "R-HSA-5669034"
            }
        },
        {
            "gwas": {
                "trait": "Crohn's disease",
                "id": "30"
            },
            "mre_study_snp": {
                "se": 0.0232,
                "eaf": 0.543391,
                "pval": 1.85994456322258e-38,
                "samplesize": 20883.0,
                "beta": 0.301402
            },
            "snp": {
                "name": "rs12692254"
            },
            "gene": {
                "name": "ATG16L1"
            },
            "protein": {
                "uniprot_id": "Q676U5"
            },
            "pathway": {
                "name": "Macroautophagy",
                "reactome_id": "R-HSA-1632852"
            }
        },
        {
            "gwas": {
                "trait": "Crohn's disease",
                "id": "12"
            },
            "mre_study_snp": {
                "se": 0.0128775,
                "eaf": 0.2812,
                "pval": 2.05210699145126e-33,
                "samplesize": 51874.0,
                "beta": 0.155114
            },
            "snp": {
                "name": "rs3197999"
            },
            "gene": {
                "name": "MST1"
            },
            "protein": {
                "uniprot_id": "P26927"
            },
            "pathway": {
                "name": "Signaling by MST1",
                "reactome_id": "R-HSA-8852405"
            }
        },
        {
            "gwas": {
                "trait": "Crohn's disease",
                "id": "12"
            },
            "mre_study_snp": {
                "se": 0.0128298,
                "eaf": 0.3529,
                "pval": 6.77797558299366e-32,
                "samplesize": 51874.0,
                "beta": 0.150794
            },
            "snp": {
                "name": "rs9264942"
            },
            "gene": {
                "name": "HLA-B"
            },
            "protein": {
                "uniprot_id": "P30486"
            },
            "pathway": {
                "name": "Interferon alpha/beta signaling",
                "reactome_id": "R-HSA-909733"
            }
        },
        {
            "gwas": {
                "trait": "Crohn's disease",
                "id": "12"
            },
            "mre_study_snp": {
                "se": 0.0128298,
                "eaf": 0.3529,
                "pval": 6.77797558299366e-32,
                "samplesize": 51874.0,
                "beta": 0.150794
            },
            "snp": {
                "name": "rs9264942"
            },
            "gene": {
                "name": "HLA-B"
            },
            "protein": {
                "uniprot_id": "P30486"
            },
            "pathway": {
                "name": "Interferon gamma signaling",
                "reactome_id": "R-HSA-877300"
            }
        },
        {
            "gwas": {
                "trait": "Crohn's disease",
                "id": "12"
            },
            "mre_study_snp": {
                "se": 0.0128298,
                "eaf": 0.3529,
                "pval": 6.77797558299366e-32,
                "samplesize": 51874.0,
                "beta": 0.150794
            },
            "snp": {
                "name": "rs9264942"
            },
            "gene": {
                "name": "HLA-B"
            },
            "protein": {
                "uniprot_id": "Q29836"
            },
            "pathway": {
                "name": "Interferon alpha/beta signaling",
                "reactome_id": "R-HSA-909733"
            }
        },
        {
            "gwas": {
                "trait": "Crohn's disease",
                "id": "12"
            },
            "mre_study_snp": {
                "se": 0.0128298,
                "eaf": 0.3529,
                "pval": 6.77797558299366e-32,
                "samplesize": 51874.0,
                "beta": 0.150794
            },
            "snp": {
                "name": "rs9264942"
            },
            "gene": {
                "name": "HLA-B"
            },
            "protein": {
                "uniprot_id": "Q29836"
            },
            "pathway": {
                "name": "Interferon gamma signaling",
                "reactome_id": "R-HSA-877300"
            }
        },
        {
            "gwas": {
                "trait": "Crohn's disease",
                "id": "12"
            },
            "mre_study_snp": {
                "se": 0.0128298,
                "eaf": 0.3529,
                "pval": 6.77797558299366e-32,
                "samplesize": 51874.0,
                "beta": 0.150794
            },
            "snp": {
                "name": "rs9264942"
            },
            "gene": {
                "name": "HLA-B"
            },
            "protein": {
                "uniprot_id": "Q31610"
            },
            "pathway": {
                "name": "Interferon gamma signaling",
                "reactome_id": "R-HSA-877300"
            }
        },
        {
            "gwas": {
                "trait": "Crohn's disease",
                "id": "12"
            },
            "mre_study_snp": {
                "se": 0.0128298,
                "eaf": 0.3529,
                "pval": 6.77797558299366e-32,
                "samplesize": 51874.0,
                "beta": 0.150794
            },
            "snp": {
                "name": "rs9264942"
            },
            "gene": {
                "name": "HLA-B"
            },
            "protein": {
                "uniprot_id": "Q31610"
            },
            "pathway": {
                "name": "Interferon alpha/beta signaling",
                "reactome_id": "R-HSA-909733"
            }
        },
        {
            "gwas": {
                "trait": "Crohn's disease",
                "id": "12"
            },
            "mre_study_snp": {
                "se": 0.0128298,
                "eaf": 0.3529,
                "pval": 6.77797558299366e-32,
                "samplesize": 51874.0,
                "beta": 0.150794
            },
            "snp": {
                "name": "rs9264942"
            },
            "gene": {
                "name": "HLA-B"
            },
            "protein": {
                "uniprot_id": "P01889"
            },
            "pathway": {
                "name": "Interferon alpha/beta signaling",
                "reactome_id": "R-HSA-909733"
            }
        },
        {
            "gwas": {
                "trait": "Crohn's disease",
                "id": "12"
            },
            "mre_study_snp": {
                "se": 0.0128298,
                "eaf": 0.3529,
                "pval": 6.77797558299366e-32,
                "samplesize": 51874.0,
                "beta": 0.150794
            },
            "snp": {
                "name": "rs9264942"
            },
            "gene": {
                "name": "HLA-B"
            },
            "protein": {
                "uniprot_id": "P01889"
            },
            "pathway": {
                "name": "Interferon gamma signaling",
                "reactome_id": "R-HSA-877300"
            }
        },
        {
            "gwas": {
                "trait": "Crohn's disease",
                "id": "12"
            },
            "mre_study_snp": {
                "se": 0.0128298,
                "eaf": 0.3529,
                "pval": 6.77797558299366e-32,
                "samplesize": 51874.0,
                "beta": 0.150794
            },
            "snp": {
                "name": "rs9264942"
            },
            "gene": {
                "name": "HLA-B"
            },
            "protein": {
                "uniprot_id": "P01889"
            },
            "pathway": {
                "name": "Neutrophil degranulation",
                "reactome_id": "R-HSA-6798695"
            }
        },
        {
            "gwas": {
                "trait": "Crohn's disease",
                "id": "12"
            },
            "mre_study_snp": {
                "se": 0.0128298,
                "eaf": 0.3529,
                "pval": 6.77797558299366e-32,
                "samplesize": 51874.0,
                "beta": 0.150794
            },
            "snp": {
                "name": "rs9264942"
            },
            "gene": {
                "name": "HLA-B"
            },
            "protein": {
                "uniprot_id": "P30480"
            },
            "pathway": {
                "name": "Interferon gamma signaling",
                "reactome_id": "R-HSA-877300"
            }
        },
        {
            "gwas": {
                "trait": "Crohn's disease",
                "id": "12"
            },
            "mre_study_snp": {
                "se": 0.0128298,
                "eaf": 0.3529,
                "pval": 6.77797558299366e-32,
                "samplesize": 51874.0,
                "beta": 0.150794
            },
            "snp": {
                "name": "rs9264942"
            },
            "gene": {
                "name": "HLA-B"
            },
            "protein": {
                "uniprot_id": "P30480"
            },
            "pathway": {
                "name": "Interferon alpha/beta signaling",
                "reactome_id": "R-HSA-909733"
            }
        },
        {
            "gwas": {
                "trait": "Crohn's disease",
                "id": "12"
            },
            "mre_study_snp": {
                "se": 0.0128298,
                "eaf": 0.3529,
                "pval": 6.77797558299366e-32,
                "samplesize": 51874.0,
                "beta": 0.150794
            },
            "snp": {
                "name": "rs9264942"
            },
            "gene": {
                "name": "HLA-B"
            },
            "protein": {
                "uniprot_id": "Q31612"
            },
            "pathway": {
                "name": "Interferon alpha/beta signaling",
                "reactome_id": "R-HSA-909733"
            }
        },
        {
            "gwas": {
                "trait": "Crohn's disease",
                "id": "12"
            },
            "mre_study_snp": {
                "se": 0.0128298,
                "eaf": 0.3529,
                "pval": 6.77797558299366e-32,
                "samplesize": 51874.0,
                "beta": 0.150794
            },
            "snp": {
                "name": "rs9264942"
            },
            "gene": {
                "name": "HLA-B"
            },
            "protein": {
                "uniprot_id": "Q31612"
            },
            "pathway": {
                "name": "Interferon gamma signaling",
                "reactome_id": "R-HSA-877300"
            }
        },
        {
            "gwas": {
                "trait": "Crohn's disease",
                "id": "12"
            },
            "mre_study_snp": {
                "se": 0.0370279,
                "eaf": 0.01883,
                "pval": 1.74702854076343e-26,
                "samplesize": 51874.0,
                "beta": 0.394341
            },
            "snp": {
                "name": "rs76906269"
            },
            "gene": {
                "name": "LRRK2"
            },
            "protein": {
                "uniprot_id": "Q5S007"
            },
            "pathway": {
                "name": "PTK6 promotes HIF1A stabilization",
                "reactome_id": "R-HSA-8857538"
            }
        },
        {
            "gwas": {
                "trait": "Crohn's disease",
                "id": "12"
            },
            "mre_study_snp": {
                "se": 0.0128549,
                "eaf": 0.3195,
                "pval": 2.17921460066021e-25,
                "samplesize": 51874.0,
                "beta": 0.133849
            },
            "snp": {
                "name": "rs11152949"
            },
            "gene": {
                "name": "PRDM1"
            },
            "protein": {
                "uniprot_id": "O75626"
            },
            "pathway": {
                "name": "Regulation of TP53 Expression",
                "reactome_id": "R-HSA-6804754"
            }
        },
        {
            "gwas": {
                "trait": "Crohn's disease",
                "id": "12"
            },
            "mre_study_snp": {
                "se": 0.0122466,
                "eaf": 0.4576,
                "pval": 1.29330215133957e-22,
                "samplesize": 51874.0,
                "beta": 0.119845
            },
            "snp": {
                "name": "rs26528"
            },
            "gene": {
                "name": "IL27"
            },
            "protein": {
                "uniprot_id": "Q8NEV9"
            },
            "pathway": {
                "name": "Interleukin-27 signaling",
                "reactome_id": "R-HSA-9020956"
            }
        },
        {
            "gwas": {
                "trait": "Crohn's disease",
                "id": "12"
            },
            "mre_study_snp": {
                "se": 0.0125708,
                "eaf": 0.3757,
                "pval": 1.67687233574859e-22,
                "samplesize": 51874.0,
                "beta": -0.122687
            },
            "snp": {
                "name": "rs13001325"
            },
            "gene": {
                "name": "IL18R1"
            },
            "protein": {
                "uniprot_id": "Q13478"
            },
            "pathway": {
                "name": "Interleukin-18 signaling",
                "reactome_id": "R-HSA-9012546"
            }
        },
        {
            "gwas": {
                "trait": "Crohn's disease",
                "id": "12"
            },
            "mre_study_snp": {
                "se": 0.0125708,
                "eaf": 0.3757,
                "pval": 1.67687233574859e-22,
                "samplesize": 51874.0,
                "beta": -0.122687
            },
            "snp": {
                "name": "rs13001325"
            },
            "gene": {
                "name": "IL18R1"
            },
            "protein": {
                "uniprot_id": "Q13478"
            },
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