A total of 3511 CAGES participants had DNA extracted and were genotyped for 599 011 common single nucleotide polymorphisms (SNPs) using the Illumina610-Quadv1 chip (Supplementary Table 1). We applied stringent quality control analyses of the genotype data and retained 549 692 of the 599 011 SNPs on the Illumina 610 chip in 3511 individuals (2115 females) (Supplementary Figure 1). Individuals were excluded from this study based on unresolved gender discrepancy, relatedness, call rate (≤ 0.95), and evidence of non-Caucasian descent. SNPs were included in the analyses if they met the following conditions: call rate ≥ 0.98, minor allele frequency ≥ 0.01, and Hardy-Weinberg equilibrium test with P ≥ 0.001. Differences in allele frequencies between the discovery and replication samples were investigated, and no sizeable deviations were observed (Supplementary Figure 1). We tested for population stratification within each cohort and excluded any outliers. The first four components from a multidimensional scaling (MDS) analysis of the SNP data, based on the remaining individuals, were included as covariates in subsequent analyses (Supplementary Figure 2). A total of 3400 and 3482 samples with both phenotypic and SNP data were available for gf and gc, respectively.
