Figure 4a shows there is considerable inter-study variability in the number of significant eQTLs even with consistent QC and analysis.19,31 With increasing sample size it appears that most expressed genes (>10,000) show evidence of local eQTL influence in peripheral blood. For NTR, the number of significant genes (q < 0.01) was 11,834, and after employing final QC steps was 9,640. Replication was checked in 1,895 unrelated samples from the Netherlands Study of Depression and Anxiety (NESDA), which had a similar sex distribution (68% female) and age range (from 18 through 65 years). Supplementary Figure 6 shows reproducibility of eQTLs between NTR and the 1,895 unrelated NESDA samples, and Supplementary Figure 7 shows regulatory feature enrichment/deficits for local eQTL SNPs.
