The HPFS and NHS cohorts were ascertained by type-II diabetes (T2D), which might affect the estimate of genetic variance because BMI is a risk factor for T2D28. We performed analyses of the variance explained by all the autosomal SNPs separately in T2D cases and controls of the HPFS and NHS cohorts, and did not observe significant differences in estimated genetic variance between cases and controls for all the three traits (Supplementary Table 10). Moreover, we estimated hG2 in the combined dataset excluding the T2D cases, and the estimate was not different from that using all samples (Supplementary Table 11). These two additional analyses show little, if any, impact of the ascertainment of T2D cases on the estimate of variance explained by the SNPs.
