Among 321 classic phenotypic associations meeting a stringent q value threshold of<0.01 (Supplementary Data 12), a few variants, such as those in Gpnmb, Comt and H2-B1, have been associated previously with disease14151617 using traditional forward genetics approaches (Supplementary Data 15), but the vast majority of variants have not been previously linked to any phenotype. Here, we provided four PheWAS examples, including two missense variants (Fh1 and Col6a5), a nonsense variant (Ahr) and a CNV (a region covering both Alad and Hdh3). In addition, we also provided three other examples in the Supplementary Note 1, including a missense variant in Entpd2 (Supplementary Fig. 4), a noncoding variant in Hcfc1r1 (Supplementary Fig. 5), and frameshift variant in Pcm1 (Supplementary Fig. 6).
