Table 2.

Results of the replication and joint analyses

						Replication phase					Discovery phase	Joint analysis
Chr	SNP	Locus	BP	A1	A2	MAF cases	MAF controls	OR	95%-CI	Preplication	Pdiscovery	Pjoint
1	rs2760524	RGS1	190797171	A	G	0.150	0.169	0.87	(0.81–0.92)	3.20 × 10–6	1.07 × 10–4	3.55 × 10–9
3	rs4680534	IL12A	161181639	C	T	0.363	0.338	1.11	(1.05–1.16)	2.81 × 10–5	6.80 × 10–5	3.08 × 10–8
12	rs1790100	MPHOSPH9/CDK2AP1	122222678	G	T	0.240	0.218	1.10	(1.04–1.16)	3.95 × 10–4	2.74 × 10–7	3.96 × 10–8
2	rs882300	CXCR4	136692725	T	C	0.431	0.460	0.91	(0.87–0.96)	9.29 × 10–5	5.17 × 10–4	4.34 × 10–7
5	rs6896969	PTGER4	40460183	A	C	0.383	0.400	0.94	(0.88–1.00)	4.11 × 10–2	1.44 × 10–7	2.80 × 10–6
10	rs1250540	ZMIZ1	80706013	G	A	0.374	0.372	1.05	(0.99–1.11)	1.18 × 10–1	9.89 × 10–6	2.31 × 10–4
6	rs9321619	OLIG3/TNFAIP3	137916101	G	A	0.464	0.478	0.94	(0.90–0.99)	2.29 × 10–2	9.34 × 10–4	2.85 × 10–4

Abbreviations: A1, minor allele; A2, major allele: BP, physical position of the SNP in build 36; chr, chromosome; MAF, minor allele frequency; OR, odds ratio; P_discovery P-value from the previous genome-wide meta-analysis study⁷ (discovery phase); P_joint, P-value obtained combining the results from the discovery and replication phase; P_replication, P-value obtained pooling together the results from all the replication samples; SNP, single-nucleotide polymorphism.

The MAF in cases and controls was calculated as average allele frequency of the minor allele weighted for the sample size of each replication collection. OR and 95% confidence intervals refer to the meta-analysis performed across all the replication collections. At each locus, the OR is stated relative to the minor allele. 95%-CI refers to the lower and upper bounds of the 95% confidence interval for the OR. All the above results are based on a fixed-effect model. The SNPs are listed in order of decreasing significance at the joint analysis.