Table 3  Characteristics of Liver eQTLs
Figure 4  Properties of All Liver eQTLs
(A) Distribution of all significant liver eQTLs across the genome in 2-cM bins. A total of 6,676 significant eQTLs were realized, representing 4,998 liver transcripts. Hotspots of nonrandom eQTL colocalization are clearly evident.
(B) Distribution of eQTLs with significant sex-specific effects. A total of 1,166 eQTLs representing 1,044 transcripts show an eQTL hotspot on Chromosome 5.
(C) Properties of eQTLs at increasing significance levels. As the threshold for significant linkage increases (p-value decreases, or LOD score increases), the proportion of cis-eQTLs (black) increases. The fraction of all eQTLs with sex effects (red) and cis-eQTLs with sex effects (blue) remains relatively constant at increasing thresholds. The dashed line indicates the genome-wide significance threshold (p < 5 × 10−5; genome-wide p < 0.05).
(D) Properties of sex-specific eQTLs at increasing significance levels. For eQTLs with significant sex effects, as with all eQTLs, the proportion of cis-eQTLs (black) increases and trans (blue) decreases as the threshold for significance increases. At the genome-wide threshold for significance (dashed line), over 70% of eQTLs with significant sex effects are trans. The distribution of all 6,676 significant eQTLs (p < 5 × 10−5) across the genome in 2 cM bins is shown in Figure 4A.