An atlas of epigenetic and transcriptomic Mendelian randomization associations


Transcriptome-wide analysis for a single trait:


Phenome-wide analysis for a single gene:


Epigenome-wide analysis for a single trait:


Phenome-wide analysis for a single CpG site:



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Summary

This web application can be used to investigate associations between genome-wide gene expression or DNA methylation with 723 complex traits by applying Mendelian randomization and genetic colocalization1. Analyses have been undertaken using whole blood-derived effects on gene expression made available by the eQTLGen consortium2 (n=31,684) and DNA methylation from GoDMC consortium3 (n=27,750). Findings from this web application can help uncover associations between genetically predicted molecular signatures and complex traits in either a transcriptome-, epigenome- or phenome-wide manner. Currently p-values for both Manhattan and PheWAS plots are based on the lead SNP SMR p-values as not all CpG sites and genes have multiple independent instruments.

Instructions

To query results from our atlas please select parameters on the left hand side of this page before clicking the 'Search Atlas' button. This will generate results in the Tables of Results.

There are 4 ways to query the results of our atlas depending on the Molecular Trait and Evaluation Type selected:

Gene & Transcriptome-wide analysis - A transcriptome-wide association study for a selected trait. Select a complex trait of interest from the drop-down menus before clicking the 'Search Atlas' button. This will evaluate all transcriptome-wide MR associations for your trait and plot results using a manhattan plot4.

Gene & Phenome-wide analysis - Phenome-wide association study for genetically predicted gene expression. Type in a Gene and click the 'Search Atlas' button. This will query the findings between your target gene and all traits in our atlas. An interactive plot5 will be generated to display -log10 p-values multiplied by the corresponding direction of effect for each result. As such, positive associations reside above -log10=0, whereras negative associations reside below. Points are grouped and coloured based on their corresponding traits subcategory.

CpG site & Epigenome-wide analysis - An epigenome-wide association study for a selected trait. Select a complex trait of interest from the drop-down menus before clicking the 'Search Atlas' button. This will evaluate all epigenome-wide MR associations for your trait and plot results using a manhattan plot4.

CpG site & Phenome-wide analysis - Phenome-wide association study for genetically predicted DNA methylation. Type in a CpG site and click the 'Search Atlas' button. This evaluate phenome-wide associations for your chosen CpG site and plots results as described above.

The Download button can be used to download a comma-separate value (csv) file for the results you have queried.

Citation

A phenome-wide Mendelian randomization study to elucidate epigenetic and transcriptomic processes which putatively mediate the effect of genetic variants on disease by Tom G Richardson, Genevieve M Leyden, Gibran Hemani, Josine L Min, The GoDMC Consortium, Tom R Gaunt, George Davey Smith and Caroline L Relton. bioRxiv (2019) doi: https://doi.org/10.1101/563379

About

For any queries please contact:

Tom.G.Richardson@bristol.ac.uk
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