Summary Statistic Data

This page describes how to access and download the summary statistic data from all 3,144 GWAS described in the paper

Elliott, L. et al (2018) https://www.nature.com/articles/s41586-018-0571-7

We have made the data available in a Dropbox folder.

The following file lists the files that contain the summary stats for the 3,144 GWAS.

BIG_summary_stat_files.xls

This file has the following columns

• ID -- integer code for IDP
• IDP -- image derived phenotype name
• LINK -- URL to file
• FILE -- file name
• COMMAND -- wget command to download file

Each of the files listed in this XLS file is a gzipped txt file (*.txt.gz) with summary stats for each of 11,734,353 SNPs. The files have one line per SNP with the following columns

• MAF -- minor allele frequency
• BETA -- estimated effect size for the alternate allele.
• SEBETA -- standard error of estimated effect size.
• PVAL -- -log10 p-value.

To reduce file sizes we provide one single file which lists the chromosome, RS ID, basepair position, reference and alternate alleles of all the 11,734,353 SNPs in each GWAS file. This file (gzipped text file) is here. positions.txt.gz

This is a file that provides the number of subjects used per IDP in the discovery cohort. The first column is the IDP number and the second column is the IDP name and the third column is the number of samples used. For a given IDP, this number is constant over all variants. The file can be downloaded from here. IDP.txt.gz

Contact

If you have any questions please email : marchini@stats.ox.ac.uk, steve@fmrib.ox.ac.uk