The new LocusZoom.org allows you to generate interactive, shareable plots of GWAS summary statistics. Building on years of experience from the developers of LocusZoom, this adds new features such as Manhattan plots, annotation options, and calculations that put findings in context. The default annotations support human datasets in builds GRCh37 or GRCh38. More annotation features are planned soon; subscribe to our mailing list to receive announcements.
This site is operated by the University of Michigan Center for Statistical Genetics.
If you have found this service useful, please cite our paper, LocusZoom.js: interactive and embeddable visualization of genetic association study results (Bioinformatics 2021).
When uploading, you can choose whether to make your dataset either public (viewable by anyone) or private (viewable only to yourself). If you make your dataset public, other people will be able to download the standardized summary statistic files that we generate during the upload process. For all datasets, interactive plotting features require that we keep a copy of the data on our servers. We make every effort to keep this secure, but if privacy is a driving issue, consider using the LocalZoom tool to generate region plots client-side instead. LocalZoom does not provide any enhanced annotation features, but it works without uploading your data.
You can delete your results from our servers at any time. The "delete this study" button may be found by clicking the "edit" link at the top of the summary page (only visible on studies that you uploaded).
LocusZoom.js is dynamic and interactive: you can plot regions up to 500 kb wide at one time, but you can explore as many regions as you wish from a single upload. The server accepts uploads of up to 1 GB (this may change in the future). A manhattan plot and list of suggested regions will also be generated for you.
Note that the size limit is the same whether you compress your file or not. You will see faster uploads- and more data- if you compress your files with gzip/bgzip before uploading!
The server attempts to handle many common GWAS formats, but we strongly recommend that you compress and tabix-index your results first. (text, gzip, or bgzip are supported) Your file should contain columns that identify key information, as described below. The data must be a tab-delimited file and be sorted by chromosome and position. The upload step will ignore any columns whose meaning is not explicitly specified. The following columns are expected:
When viewing any LocusZoom plot on this site, you will be offered the option to "add [a] tabix-indexed datafile" to the plot. This allows you to compare the plot in front of you with other information of interest, without having to share sensitive or private information. Several types of track can be added. Inspired by LocalZoom, the files will remain on your local computer (they will not be uploaded, and will vanish when the page is refreshed). Remote files (such as an S3 bucket) are also supported, so long as they follow the format instructions.
The use of Tabix allows region queries for files of any size, but it does require that the files be prepared carefully before use. Some files (especially PLINK 1.9 LD) can be finicky to generate or require additional processing. We have gathered detailed instructions for how to run each step of the required programs, along with other format information. These instructions also cover how to configure cloud storage providers (Google Cloud or S3), so that you can host your own files at a remote URL without needing to manually configure an entire web server.
Sometimes, a region plot will be missing Linkage Disequilibrium (LD) information, and all points will be shown in grey. The three most common reasons are as follows:
This site uses an LD reference panel based on 1000G data, with several sub populations available. Missing variants are most commonly a problem for build 37, which uses an older version of this reference panel. As of Summer 2020, build GRCh38 datasets use an improved 1000G LD panel based on deep whole-genome sequencing. Although we are exploring the possibility of additional LD reference panels, this is non-trivial due to restrictions on public sharing of data.
Alternatively, the "add tabix file" feature allows you to generate your own LD and add it to the plot. Because LD is sometimes considered sensitive information, we explicitly do not support uploading LD data to our server; each person you are sharing the plot with will need to add their own LD from a local file (or remote URL). We welcome suggestions for how to make this more reusable in the future.
Sometimes, it may be useful to share a GWAS with a collaborator, without having to make it public for everyone. This service allows you to generate private links that can be sent to trusted collaborators. These secret links allow view-only access to all summary and region plots. Sharing features can be accessed from the "share" link on top of the GWAS summary page.
The new LocusZoom.org is still evolving, and we welcome your feedback about what features to add next. Please consider answering our user survey, or contact us directly.
There are several ways to reach us, including our user group and public bug tracker. For questions involving security or sensitive data, we may be reached at email@example.com.
The new LocusZoom.org emphasizes interactive plots and comparisons across data. However, there are times when you may wish to do something extremely specialized that is not possible on a general purpose web server. Here are some alternatives: