Table 1.

Summary of results from this study for the 4 regions showing evidence of replication, listing each SNP under consideration, their position (in bp) and minor allele frequency (MAF); the per-allele OR (based on the minor allele) and p-value are given for this GWA study, for the meta-analysis of the replication data sets (from the Houston GWA study, the Australian GWA study and UK/Netherlands replication samples) and for the combined genome-wide and replication analyses. The Houston GWA study and the Australian study both used a different array to the current study for at least some samples, so some of their results presented here include imputed data. Further genotyping was conducted in the UK and Netherlands replication samples for SNPs with positive support from the GWA replication data. All meta-analyses are based on a fixed effects model with the exception of those for CCND1, marked with an asterisk, where random effects analysis was used because of the observed heterogeneity. Supplementary Table 3 is a fuller version of this table.

SNP	Chromosome	Position	Allele	MAF	GenoMEL Genome-wide		Replication samples (genotyped + imputed)		Genome-wide plus replication samples (genotyped + imputed)		Postulated gene
					OR	p	OR and 95% CI	P-value	OR and 95% CI	P-value
rs13016963	2	201852173	A	0.37	1.18	5.68 × 10−7	1.11 (1.06, 1.18)	9.2 × 10−5	1.14 (1.09, 1.19)	8.6 × 10−10	CASP8
rs1485993	11	69071595	A	0.37	1.19	4.15 × 10−7	1.07 (1.01, 1.13)	0.017	1.11 (1.04, 1.18)*	0.0012	CCND1
rs1801516	11	107680672	A	0.13	0.79	4.80 × 10−7	0.87 (0.78, 0.90)	3.4 × 10−4	0.84 (0.78, 0.90)	3.4 × 10−9	ATM
rs45430	21	41667951	G	0.39	0.85	5.60 × 10−7	0.91 (0.86, 0.96)	4.2 × 10−4	0.88 (0.85, 0.92)	2.9 × 10−9	MX2

^*Using random effects