After standard quality controls (removal of samples from individuals of suspected non-European descent, samples with call rate <95% and checks on reported sex status, cryptic relatedness, autosomal heterozygosity rate check, monomorphic SNPs or call rate <95%, no genomic position info or redundant SNPs, P value for deviation from Hardy-Weinberg equilibrium <0.0001, genotyping call rate <95%, fewer than two heterozygotes present, mismatching alleles with the 1000 Genomes Project (even after allowing for strand), imputation was performed using MaCH53,54 and minimac (http://genome.sph.umich.edu/wiki/Minimac) using the European panel of the 1000 Genomes Project (March 2012: Integrated Phase I haplotype release version 3, based on the 2010 November data freeze and 14 March 2012 haplotypes). We used the resulting 5,878,211 SNPs and 576,942 indels with good postimputation quality (Rsq > 0.50) and minor allele frequency (MAF) of at least 5%.
