Real data application results summary.

Number of jointly and marginally associated SNPs when systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA), and Crohn’s disease (CD) and ulcertive colitis (UC) GWAS are integrated with the GenoSkyline (GS) and GenoSkylinePlus (GSP) annotations when jointly and individually analyzed using the multi-GPA-Tree, the LPM and the GPA-Tree approach. All analysis included 492, 557 SNPs and 7 tissue-specific GS and 10 blood-related cell-type specific GSP annotations. Inference for marginal and joint associations are based on global FDR control at the nominal level of 0.05. For LPM, annotation enrichment is done separately for P1 and P2, and reported annotations are those with p-value <0.05 for both P1 and P2.