Manhattan plots of GWAS results for four binary phenotypes with various case-control ratios in the UK Biobank.
GWAS results from SAIGE, SAIGE-NoSPA(asymptotically equivalent to GMMAT) and BOLT-LMM are shown for A. coronary artery disease (PheCode 411, case:control = 1:12, N = 408,458), B. colorectal cancer (PheCode 153, case:control = 1:84, N = 387,318), C. glaucoma (PheCode 365, case: control = 1:89, N = 402,223), and D. thyroid cancer (PheCode 193, case:control=1:1138, N = 407,757). N: sample size. Blue: loci with association p-value < 5×10−8, which have been previously reported, Green: loci that have association p-value < 5×10−8 and have not been reported before. Since results from SAIGE-noSPA and BOLT-LMM contain many false positive signals for colorectal cancer, glaucoma, and thyroid cancer, the significant loci are not highlighted. The upper dashed line marks the break point for the different scales of the y axis and the lower dashed line marks the genome-wide significance (p-value = 5×10−8).