Table 2

Stage 1, Stage 2 and combined Stage 1 and Stage 2 samples association results for risk of coronary artery disease at single nucleotide polymorphisms in 9p21 with p<1e–04 in the combined sample

Single nucleotide polymorphism	Allele		Stage	Genotypes minor homozygous/heterozygous/major homozygous		Minor allele frequency		OR for risk allele (95% CI)	p Value
Single nucleotide polymorphism	Minor	Risk	Stage	Control	Case	Control	Case	OR for risk allele (95% CI)	p Value
rs6475606	C	T	S1	24/124/120	13/80/132	0.32	0.24	1.55 (1.16 to 2.07)	3.24e–03
			S2	123/450/474	98/458/580	0.33	0.29	1.22 (1.08 to 1.39)	2.00e–03
			S1&S2	147/574/594	111/538/712	0.33	0.28	1.27 (1.13 to 1.43)	5.75e–05

rs4977574	G	G	S1	44/133/91	63/117/45	0.41	0.54	1.71 (1.31 to 2.22)	6.74e–05
			S2	199/522/345	274/569/315	0.43	0.48	1.22 (1.08 to 1.37)	1.27e–03
			S1&S2	243/655/436	337/686/360	0.43	0.49	1.29 (1.16 to 1.44)	4.61e–06

rs2891168	G	G	S1	43/134/91	63/116/45	0.41	0.54	1.73 (1.32 to 2.25)	5.16e–05
			S2	199/524/351	274/569/316	0.43	0.48	1.23 (1.09 to 1.38)	7.59e–04
			S1&S2	242/658/442	337/685/361	0.43	0.49	1.3 (1.17 to 1.45)	2.27e–06

rs1333042	A	G	S1	27/130/106	14/90/119	0.35	0.26	1.53 (1.15 to 2.04)	3.82e–03
			S2	156/473/455	122/490/555	0.36	0.31	1.23 (1.09 to 1.39)	1.04e–03
			S1&S2	183/603/561	136/580/674	0.36	0.31	1.27 (1.13 to 1.42)	3.71e–05

rs1333048	C	C	S1	55/134/76	71/119/35	0.46	0.58	1.68 (1.29 to 2.19)	1.38e–04
			S2	232/515/326	310/574/273	0.46	0.52	1.26 (1.12 to 1.42)	1.28e–04
			S1&S2	287/649/402	381/693/308	0.46	0.53	1.32 (1.18 to 1.47)	4.95e–07

rs1333049	C	C	S1	54/137/76	72/118/33	0.46	0.59	1.75 (1.34 to 2.29)	4.51e–05
			S2	232/519/334	309/574/282	0.45	0.51	1.25 (1.12 to 1.41)	1.50e–04
			S1&S2	286/656/410	381/692/315	0.45	0.52	1.32 (1.19 to 1.47)	3.08e–07

For each SNP, the ORs (with 95% CIs) and p values represent the RR of CAD associated with each copy of the risk allele. Results are based on a trend test (1 degree of freedom) with adjustment for age, sex and, in the combined sample, stage. The minor allele frequency is defined in the controls and its frequency in that group as well as the case sample is reported. Cluster plots for each single nucleotide polymorphisms have been visually inspected and are shown in supplementary figure 4.
S1, Stage 1; S2, Stage 2; S1&S2, combined Stage 1 and Stage 2.