QQ plot and Box plot of the interactions identified in the RCG study.

<p><b>A</b>) QQ plot for interaction tests between all pairs of 304 candidate SNPs in RCG. <b>B</b>) Boxplot of HDL-C levels for the nine genotype combinations of rs1532085 and rs12980554, the pair of SNPs that exhibit the most significant gene-gene interaction in this study. The interaction is dominated by the combination of AA genotype in both SNPs.</p

Top SNPs (FDR = 0.25) interacting with rs1532085 in affecting HDL-C levels in ARIC.

a<p>dbSNP build 137.</p>b<p>Difference in R square values between the model with the interaction and the model with SNP rs1532085 alone (for which R square is 0.65%), denoting the additional variance in HDL-C levels that is captured by the interaction alone.</p

QQ plot for interaction tests between rs1532085 and genome-wide LD-pruned SNPs in the ARIC study.

<p>The plot and analysis in main text point to a deviation of the <i>P</i> values for four independent SNPs, which are detailed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092469#pone-0092469-t001" target="_blank">Table 1</a>.</p

Significant interactions on HDL-C in multi-ethnic cohorts.

a<p>EA denotes European American; HA denotes Hispanic American; AA denotes African American.</p>b<p>Build 37.1 (GRCh37).</p>c<p>U indicates upstream of; D indicates downstream of.</p>d<p><i>P</i>-value after Bonferroni correction.</p

Additional file 1: Table S1. of Discovery and replication of SNP-SNP interactions for quantitative lipid traits in over 60,000 individuals

Discovery results for all models that passed replication thresholds for MEF analysis. Column header definitions provided at the end. Table S2. Discovery results for all models that passed replication thresholds for Biofilter analysis. Column header definitions provided at the end. (PDF 1649 kb