Genotyping was conducted using the Human670-QuadCustom Illumina BeadChip (Illumina, Inc., San Diego, CA, USA) at the Wellcome Trust Sanger Institute (Kaprio, 2013). Quality control steps included removing SNPs with minor allele frequency < 1%, genotyping success rate < 95%, or Hardy-Weinberg equilibrium p < 1 × 10−6, and removing individuals with genotyping success rate < 95%, a mismatch between phenotypic and genotypic gender, excess relatedness (outside of known families), and heterozygosity outliers. Genotypes were imputed to the 1000 Genomes Phase I (v3) reference panel using ShapeIT (Delaneau et al., 2012) for phasing and IMPUTE2 (Howie et al., 2009) for imputation. Prior analyses indicated a single dimension of ancestry in the sample (Meyers, 2012). Although a single dimension of ancestry does not preclude variation along this dimension, we note that fine-scale population substructure is less of an issue for common variants (versus rare variants), especially in the present sample given the relatively longer LD blocks that make the Finnish population more homogenous than other populations of mixed European ancestry. We also note that in supplementary analyses of the first 10 ancestry
