Table 2

The Kolmogorov-Smirnov (KS) test for AP p value distributions of the interaction analysis with the HLA-DRB1 SE alleles and risk or non-risk SNPs in EIRA and NARAC imputed data

Case–control group	SNP group	Number of initial input SNPs	Number of SNPs after cut-off *	% of SNPs analysed	Number of SNPs with AP p<0.05	% of analysed SNPs with AP p<0.05	D^+value from KS test (risk vs no-risk)†	Group of SNPs with enrichment of significant interactions
EIRA	Risk	241 759	160 358	66.33	39 518	24.64	0.354	Risk
	No risk	4 515 110	2 979 344	65.99	83 287	2.80	0.354	Risk
NARAC	Risk	787 499	209 890	26.65	31 992	15.24	0.247	Risk
	No risk	8 244 955	1 916 701	23.25	64 012	3.44	0.247	Risk

↵*Interaction was estimated using sex and the 10 first eigenvectors as covariables. A minimum of five individuals in each of the four combinations that formed the basis for the OR calculations was required.
↵†The alternative hypothesis for KS test was that the empirical cumulative distribution function (ECDF) of AP p values for risk SNPs lies above that of non-risk SNPs (figure 2). KS test p<2.2e-16 for both EIRA and NARAC. As mentioned in the Materials and methods section, these KS test p values are lower than the machine precision, meaning that when the precise p value was calculated the result was 0.
AP, attributable proportion; EIRA, epidemiological investigation of rheumatoid arthritis; NARAC, North American rheumatoid arthritis consortium; SE, shared epitope; SNP, single nucleotide polymorphism.