A few studies have shown that breast cancer could arise from epithelial cells [19, 20]. The connections between breast cancer and muscle as well as GI tract have also been previously suggested [21, 22]. In addition, studies have suggested that GI can be used as diagnostic and treatment target for type-II diabetes, Crohn’s disease, and celiac disease [23–25]. Furthermore, the connection between immune system and Crohn’s disease, celiac disease and rheumatoid arthritis have been extensively studied in literature [26–28]. Next, we evaluated the effectiveness of proposed empirical effect size prior in three diseases (i.e. CD, CEL, and RA) with well-powered testing cohorts (N>2,000). Interestingly, despite the highly variable enrichment results in training datasets, integrative effect size prior could effectively identify SNPs with large effect sizes and consistent effect directions in independent validation cohorts (Fig 2B and 2C).
