Wellcome Centre for
Integrative Neuroimaging (WIN/FMRIB), Oxford, UK
Department of Statistics and Actuarial Science, Simon Fraser University, Canada
Led by Lloyd T. Elliott (SFU) and Stephen Smith (Oxford)
Interactive PheWeb server live here
This open data server contains results from GWAS of almost 4,000 imaging-derived phenotypes from the multimodal brain imaging in UK Biobank. It is a major update to the original BIG server, using data from the 40,000 subject imaging data release from early 2020. The discovery sample size was 22,138 and the replication sample 11,086. Chromosomes 1:22 and X are included, resulting in associations with 17,103,079 SNPs.
The work was funded by Wellcome Trust. Compute resources were provided by the Oxford Biomedical Research Computing (BMRC) facility (a joint development between Oxford's Wellcome Centre for Human Genetics and Big Data Institute, supported by Health Data Research UK and the NIHR Oxford Biomedical Research Centre). This work was conducted in part using the UK Biobank Resource under Application Number 8107.
A preprint on the work is on bioRxiv (and see overview of Methods below).
BIG40 24/04/20 Initial release. For a short period this will remain available here.
BIG40 29/06/20 Minor update with improved filtering on X chromosome SNPs, and provision of sample sizes for the pseudoautosomal and non-psuedoautosomal regions of the X chromosome.
BIG40 22/07/20 Minor correction to table of local peak activations (ChrX beta values were incorrect by factor of 2).
BIG40 15/10/20 Added summary stats for all 33k (disco+repro) subjects combined.
Interactive PheWeb server: 33k subjects (discovery+replication pooled) and 22k subjects (discovery only)
Table of local-peak associations (-Log10(P) > 7.5): Online table / Raw text
Table of IDPs
(imaging-derived phenotypes) with individual IDPs' Manhattan
This includes names and descriptions of all IDPs, and categorisations into 16 structural and functional IDP categories (plus 1 QC category).
The table also includes links to a Manhattan plot for each IDP (column 1), and links to each IDP's UKB Showcase variable page (column 2).
The rightmost columns show the exact sample sizes per IDP, which vary slightly due to different patterns of missing data for different imaging modalities. Sample sizes for X chromosome associations also vary due to additional X chromosome exclusions, these are also shown in the "par" and "nonpar" columns. Separate values of N are given for the discovery dataset ("disc"), reproduction data ("rep") and all subjects combined ("all").
Combined PDF with all Manhattan plots (3,935 pages, 0.75GB)
Table of all variants (SNPs,
Compressed raw text
table download only (due to size)
This has the following information for each variant: chr rsid pos a1 a2 af info
Summary stats downloads
Sumstats from 33k subjects (discovery and replication datasets combined)
The download for IDP 1 is: release2/stats33k/0001.txt.gz
The download can be automated with curl: curl -O -L -C - https://open.win.ox.ac.uk/ukbiobank/big40/release2/statsi33k/0001.txt.gz
Sumstats from 22k discovery-sample subjects
Use links such as: release2/stats/0001.txt.gz