The peak-SNPs for these eQTLs showed a full spectrum of minor allele frequencies with a skew toward relatively rare variants (MAF < 5%) (Supplemental Fig. 3). This indicates that the inclusion of rare variants in the 1000G imputation reference panel does help identify their contribution to eQTLs. Many low-frequency variants explain a large fraction of the expression trait variance (Supplemental Fig. 4), some of which can account for 30%–50% of the total variation in an expression trait. This suggests that the application of 1000G SNP-based imputation to existing GWASs may resolve part of the missing heritability complex traits.
