Legacy copy of original Oxford Brain Imaging Genetics Server

This is a copy of the data from BIGv2, originally hosted at http://big.stats.ox.ac.uk; unless you specifically need to access this original version of the data,
we recommend that instead you access the updated and expanded data from BIG40, at https://open.win.ox.ac.uk/ukbiobank/big40/

UK Biobank Brain Imaging Data

The primary source is results from 3,143 GWAS of Brain Imaging Derived Phenotypes (IDPs) measured on 9,707 participants of the UK Biobank study. Association analysis was carried out using BGENIE and is described in full in this paper: Elliott, L. et al (2018) https://www.nature.com/articles/s41586-018-0571-7

The genetic data and brain imaging data underlying this study are described in the following papers
Bycroft, C. et al (2018) https://www.nature.com/articles/s41586-018-0579-z
Miller, K. et al (2016) http://www.nature.com/neuro/journal/v19/n11/full/nn.4393.html

This project is a collaboration between:
Prof Jonathan Marchini, Department of Statistics, University of Oxford
Prof Stephen Smith, FMRIB, Wellcome Centre for Integrative Neuroimaging, University of Oxford

Allele coding, SNP effect sizes and p-values

For each SNP two alleles are reported with two alleles REF and ALT. So for example, at this SNP http://big.stats.ox.ac.uk:/variant/6:37161391-T-C the REF allele is T and the ALT allele is C. The browser also provides effect sizes and standard errors for each SNP tested against each phenotype. In all studies, the effect allele is the ALT allele. Consequently, the SNP effect sizes refer to the change in phenotype (quantitative traits) or log-odds (binary traits) corresponding to possession of an additional copy of the ALT allele.

A full interpretation, or comparison with other studies, also requires knowledge of any transformations performed on the phenotypes which are described in the references cited above. In particular, note that GWAS results for the UKBiobank phenotypes produced by the Neale lab are all based on transformed phenotypes.

Change log

17 Oct 2017 : Release of version 1 of the browser containing data from: Elliott, L. et al (2018) https://www.nature.com/articles/s41586-018-0571-7

06 Dec 2017 : Release of version 2 of the browser (these were just changes to the interactive browser, no longer supported).

Contact

For questions about this browser please email:
Sinan Shi ([email protected])
Prof Jonathan Marchini ([email protected])
Prof Steve Smith ([email protected])

Download

You can use curl to download the summary stats for the 3,143 IDPs' GWAS. These run from 0001 to 3146 (2714, 3139 and 3140 do not exist as they were removed originally).

The download for IDP 1 is: https://open.win.ox.ac.uk/ukbiobank/big40/BIGv2/0001.txt.gz
The download can be automated with curl: curl -O -L -C - https://open.win.ox.ac.uk/ukbiobank/big40/BIGv2/0001.txt.gz

Each of the files 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

We also provide a file giving 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