Table 4. Replication of conditional analysis.

			Minor/MajorAllele*	Replication 843 cases, 856 controls									Pooled NGRC & Replication 2843 cases, 2842 controls
				MAFCase	MAFControl	HWEP	Unconditioned		Conditioned on SNP1		Conditioned on SNP4		MAFCase	MAFControl	HWEP	Unconditioned		Conditioned on SNP1		Conditioned on SNP4
	SNP	BP					OR	P	OR	P	OR	P				OR	P	OR	P	OR	P
SNP1	rs3129882	32517508	G/A	0.45	0.41	0.69	1.20	0.006	-	-	1.15	0.04	0.46	0.40	0.98	1.28	3×10−10	-	-	1.23	6×10−7
SNP3	rs2844505	31547042	G/A	0.26	0.24	0.18	1.04	0.32	-	-	-	-	-	-	-	-	-	-	-	-	-
SNP4	rs9268515	32487273	C/G	0.20	0.23	0.29	1.25	0.004	1.19	0.04	-	-	0.17	0.21	0.96	1.28	2×10−6	1.18	3×10−3	-	-

*Odds ratios (OR) were calculated for the risk allele (shown in bold).

In the replication dataset, SNP1 and SNP3 were genotyped, SNP2 was not genotyped and did not impute, SNP4 was imputed (info score = 0.95). We used imputed genotype probabilities in the R software, adjusting for age and sex for replication, and adjusting for age, sex and study for pooled data. Replication P values are one sided [28] given the directionality of the hypothesis; P values for pooled NGRC and replication are two sided.