We used 3,805 genotypes that represent distinct haplotype blocks in the BXD family to perform PheWAS against 4,230 classic traits as well as 602,746 endophenotypic traits from 16 distinct tissues (Fig. 1a and Supplementary Data 1 and 2). This analysis yielded ∼14 million genotype-to-phenome correlations and ∼2.0 billion genotype-to-endophenotype correlations. A total of 95 genotypes are significantly associated with 321 phenotypes, corresponding to 108 phenotypic groups, at a stringent q value threshold of <0.01 (Supplementary Data 12). In addition, we performed differential expression analyses between the B6 and D2 strains for each association by using transcripts from 16 tissues (Supplementary Data 2) and proteins from hippocampus (Supplementary Data 13).
