PMC

Flowchart of the quality control and analysis steps for the discovery and replication phases

Results for the Biofilter analysis of TG. Showing results for the models that passed the replication threshold of p < 3.0 × 10–5. Orig# and prox# designate models that were identified in the discovery cohort and those identified via proxy (i.e. both SNPs in high LD with SNPs from orig. Models), respectively. V1 and V2 are the two SNPs in the model; arrow in likelihood ratio test (LRT) row denotes direction of effect

Pairwise r² values for SNPs in top models for main effect filtering (MEF) analysis of HDL-C levels. The numbers in the boxes are r² values and darker shading indicates higher LD. The numbers below the SNPs are an indicator of location in this region. Correlation patterns indicate three sets of SNPs and two interaction signals based on replication results (Set 1 x Set 2 and Set 2 x Set 3)

Results for the main effect filter (MEF) analysis of LDL-C. Showing results for the models that passed the replication threshold of p < 3.0 × 10–5. Orig# and prox# designate models that were identified in the discovery cohort and those identified via proxy (i.e. both SNPs in high LD with SNPs from orig. Models), respectively. V1 and V2 are the two SNPs in the model; arrow in likelihood ratio test (LRT) row denotes direction of effect

Results for the main effect filter (MEF) analysis of TG. Showing results for the models that passed the replication threshold of p < 3.0 × 10–5. Orig# and prox# designate models that were identified in the discovery cohort and those identified via proxy (i.e. both SNPs in high LD with SNPs from orig. Models), respectively. V1 and V2 are the two SNPs in the model; arrow in likelihood ratio test (LRT) row denotes direction of effect

Results for the main effect filter (MEF) analysis of HDL-C. Showing results for the models that passed the replication threshold of p < 3.0 × 10–5. Orig# and prox# designate models that were identified in the discovery cohort and those identified via proxy (i.e. both SNPs in high LD with SNPs from orig. Models), respectively. V1 and V2 are the two SNPs in the model; arrow in likelihood ratio test (LRT) row denotes direction of effect

Results for the main effect filter (MEF) analysis of TC. Showing results for the models that passed the replication threshold of p < 3.0 × 10–5. Orig# and prox# designate models that were identified in the discovery cohort and those identified via proxy (i.e. both SNPs in high LD with SNPs from orig. Models), respectively. V1 and V2 are the two SNPs in the model; arrow in likelihood ratio test (LRT) row denotes direction of effect

Pairwise r² values for SNPs in top models for the main effect filtering (MEF) replication analysis of plasma triglyceride (TG) levels. The numbers in the boxes are r² values and darker shading indicates higher LD. The numbers below the SNPs are an indicator of location in this region. Correlation patterns indicate a single signal representing an interaction between rs180327 (or a correlated functional variant) and the other variants for the four models that include this SNP