Since the SMR analysis assumes that the instrument (top cis-eQTL) has a strong effect on the exposure (gene’s expression level), only probes with at least one cis-eQTL at PeQTL (a p value from the eQTL study indicating the significance of the eQTL associated with the gene expression) smaller than 5 × 10−8 in the cis-eQTL region were included in the eQTL summary data (hg19). We excluded cis-eQTL with MAF < 0.01 and cis-eQTL in the MHC region because of the complexity of LD patterns in this region [22]. After data processing, there were 5967 probes left. So the genome-wide significance level for SMR test was Psmr < 8.4 × 10−6 (0.05/5967, Bonferroni Correction).
