Quantile-Quantile plot

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Quantile-Quantile plot Manhattan plot of HDL cholesterol GWAS Genome-wide significance (p-value = 5 x 10-8) Suggestive association (p-value = 1 x 10-5) -log10(p-value) 0 2 4 6 8 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 Chromosome Quantile-Quantile plot Genomic inflation (λ) = 1.01696 0 1 2 3 4 5 6 Observed –log10(P) 0 1 2 3 4 5 6 Expected –log10(P) Supplementary Figure S1. Manhattan and quantile-quantile plot for CAVAS GWAS results of HDL cholesterols

Quantile-Quantile plot Manhattan plot of LDL cholesterol GWAS Genome-wide significance (p-value = 5 x 10-8) Suggestive association (p-value = 1 x 10-5) -log10(p-value) 0 2 4 6 8 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 Chromosome Quantile-Quantile plot Genomic inflation (λ) = 1.04519 0 1 2 3 4 5 6 Observed –log10(P) 0 1 2 3 4 5 6 Expected –log10(P) Supplementary Figure S2. Manhattan and quantile-quantile plot for CAVAS GWAS results of LDL cholesterols

Quantile-Quantile plot Manhattan plot of Triglycerides GWAS Genome-wide significance (p-value = 5 x 10-8) Suggestive association (p-value = 1 x 10-5) -log10(p-value) 0 2 4 6 8 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 Chromosome Quantile-Quantile plot Genomic inflation (λ) = 1.0000 0 1 2 3 4 5 6 Observed –log10(P) 0 1 2 3 4 5 6 Expected –log10(P) Supplementary Figure S3. Manhattan and quantile-quantile plot for CAVAS GWAS results of Triglycerides

Quantile-Quantile plot Manhattan plot of total cholesterols GWAS Genome-wide significance (p-value = 5 x 10-8) Suggestive association (p-value = 1 x 10-5) -log10(p-value) 0 2 4 6 8 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 Chromosome Quantile-Quantile plot Genomic inflation (λ) = 1.01247 0 1 2 3 4 5 6 Observed –log10(P) 0 1 2 3 4 5 6 Expected –log10(P) Supplementary Figure S4. Manhattan and quantile-quantile plot for CAVAS GWAS results of Total cholesterols

Supplementary Figure S5 Supplementary Figure S5. Principal Component Analysis plots for CAVAS (Red), KARE (Blue), and HEXA (Yellow) with HAPMAP populations (Purple).