Imputation was performed by using ShapeIT [35] in pre-phasing and IMPUTE2 [36] for genotype imputation, with the 1000 Genomes Phase I integrated variant set release (v3) reference panel. The posterior probability threshold for “best-guess” imputed genotypes was 0.9. Genotypes below the threshold were set to missing. Genotypes for altogether 6,729,635 SNPs were available for analysis.
