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Fig. 2 | Genome Biology

Fig. 2

From: Primo: integration of multiple GWAS and omics QTL summary statistics for elucidation of molecular mechanisms of trait-associated SNPs and detection of pleiotropy in complex traits

Fig. 2

A conceptual illustration of the conditional association analysis of Primo. Consider a joint analysis of GWAS summary statistics and summary statistics of eQTL, meQTL, and pQTL. In a gene region harboring trait-associated SNPs, there is a GWAS SNP of interest (red/blue dot) and two other confounding SNPs—the lead SNPs for eQTL and meQTL (green cross). Before conditional association analysis, the GWAS SNP is estimated to be associated with cis expression, methylation, and protein levels. After adjusting for the two lead omics SNPs, the GWAS SNP is no longer associated with cis expression levels (blue dot) but is still estimated to be a me- and pQTL

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