This PDF file includes:

• Note S1. Theoretical derivation of vQTL as a consequence of GEI
• Note S2. The Bartlett’s test, the FK test, and the DGLM test
• Note S3. Rank-based inverse-normal transformation
• Note S4. The effective number of independent traits
• Note S5. Definitions of the three environmental factors—PA, SB, and smoking
• Note S6. Expected inflation in the Levene’s test statistic due to phantom vQTL effect
• Note S7. Acknowledgments
• Fig. S1. Evaluation of statistical methods and phenotype processing strategies for the vQTL analysis by simulation based on a single-SNP model.
• Fig. S2. Phenotypic correlations among 13 quantitative traits, and PA and SB measures in the UKB.
• Fig. S3. Genome-wide vQTL and QTL analyses for 13 traits in the UKB.
• Fig. S4. Quantile-quantile plots of vQTL associations for the 13 UKB traits.
• Fig. S5. Enrichment of GEI effects among the 75 vQTLs compared with a random set of QTLs using the raw phenotypic values.
• Fig. S6. Comparison of the Young et al. method with the Levene’s test by vQTL simulation.
• Fig. S7. Excluding two alternative explanations for vQTL signals: Phantom vQTLs and epistasis.
• Table S1. Descriptive summary of (A) the quantitative traits and (B) the environmental data used in this study from the UKB.
• Table S2. Seventy-five experiment-wise significant vQTLs for nine UKB traits.
• Table S3. GEI examples.
• References (68–75)

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