Autosomal genotypes were available for all UKB individuals in the present study (n = 24 337). Pre-imputation QC, phasing and imputation are described elsewhere27. In brief, prior to phasing, multiallelic SNPs or those with MAF ≤ 1% were removed. Phasing of genotype data was performed using a modified version of the SHAPEIT2 algorithm28. Imputation to a reference set combining the UK10K haplotype and 1000 Genomes Phase 3 reference panels29 was performed using IMPUTE2 algorithms30,31. A further QC protocol was then applied at the Wellcome Trust Centre for Human Genetics before the data was released, as described elsewhere32. The analyses presented here were restricted to autosomal variants with an imputation INFO score ≥ 0.9 and MAF ≥ 0.5%.
