pGWAS server

Supplemental Files

Dataset	File name	Size	Description
Supplemental Figure 6	SupplementalFigure6.pdf.zip	34.39M	Regional association plots for all significant cis and trans associations using 1000 Genome Project imputed genotypes in KORA (discovery cohort). Linkage disequilibrium information is based on within-population observations. Functional annotations of variant effects provided by SNiPA v3.1. File contains individual PDF files stored in a ZIP archive.
	SupplementalFigure6.png.zip	82.54M	File contains individual PNG files stored in a ZIP archive.
	SupplementalFigure6.tsv.zip	421.61M	File contains the association data used to generate the plots as tab-separated text files stored in a ZIP archive.
Supplemental Figure 8	SupplementalFigure8.zip	5.60M	Histograms and boxplots using three different scaling methods (raw, log₂, inverse-normal) with association data and allele counts for all 539 significant SNP-protein associations in KORA and 462 replication attempts in QMDiab. File contains PDF files stored in a ZIP archive.
Supplemental Figure 9	SupplementalFigure9.pdf	18.59M	SNiPA annotations ("SNiPA cards") for 435 (out of 451) sentinel SNPs that are contained in SNiPA v3.1. Annotations are based on the 1000 Genome Project phase 3 version 5 variant set and Ensembl 82 annotations. File contains all SNiPA cards merged into a single PDF file.
	SupplementalFigure9.pdf.zip	22.01M	File contains individual PDF files stored in a ZIP archive.
All associations	suhre.pgwas.koraf4.tar	9.62G	TAR archive contains a gzipped genome-wide association results file for each of the 1,124 protein levels (inverse-normal distributed) as determined in the discovery cohort (KORA F4), sorted by p-values in descending order. Columns 1 and 2 depict the Somalogic sequence ID and the target's name (see list of targets), columns 3 and above are in PLINK output format (CHR, SNP, BP, A1, TEST, NMISS, BETA, STAT, P; see PLINK documentation).
Probe annotations	probeanno.json	2.68M	File contains the mapping of Somalogic-IDs to targets as well as further annotations. File format: JSON.
	probeanno.tsv	1.72M	JSON-file reformatted as tab-delimited text file. Multiple entries are separated by "\|".
This webserver	server.20180628.tar.gz	882.26M	Run a copy of this website on your (local) web server (requires PHP support enabled; tested under PHP v5.6). Note that the supplementary files listed above are not part of the archive. We recommend Docker (available for Windows, macOS, and Linux) to run a local web server. Install Docker according to the Docker tutorial. On a console/command line prompt, change into the directory where you extracted the contents of server.20180628.tar.gz. If you are using Linux or macOS, enter sudo docker run -p 80:80 -v "$PWD":/var/www/html php:5.6-apache If you are using Windows' command prompt (cmd), enter docker run -p 80:80 -v %cd%:/var/www/html php:5.6-apache When you run this command the first time, it takes a few minutes to download the Docker template. To access your local version of this website, open the web page http://localhost/. To stop the local web server, press Ctrl+C in the console window.