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. Author manuscript; available in PMC: 2011 Nov 30.
Published in final edited form as: Ann Appl Stat. 2011 Sep 1;5(3):2052–2077. doi: 10.1214/11-AOAS469

Fig. 7.

Fig. 7

Log10 p-values (y-axis) of joint association test between SNPs in the nonclass II MHC region (x-axis) and SNPs in the MHC class II region (32.5–32.8 Mb), with main effects of the MHC class II SNPs subtracted and conditioned on 78 T1D associated haplotypes in HLA-DR-DQ. Each SNP has multiple p-values, shown as grey dots, corresponding to interactions with different MHC class II SNPs. The black line for the SNP indicates the −log 10 p-value of the nonclass II SNP’s main effect. A cutoff of 10−5 for the p-values, shown as the dashed line, corresponds to roughly one false positive among all tests.