Table 2.

Results from the replication analysis of the most promising 12 SNPs

SNP	Locus	Chr	Risk Allele	WTCCC nsSNP Screena	Replication Stage1b	Replication Stage 2c	Replication Analysis Combined	Combined Analysisd		RAF Case	RAF Control	Breslow Day Test
				p-value	p-value	p-value	p-value	p-value	Odds Ratio (CI 95%)			p-value
rs3748816	MMEL1	1	T	1.63×10−3	1.34×10−3	0.0178	3.57×10−4	3.54×10−6	1.16 (1.09–1.24)	0.696	0.660	0.650
rs2304497	ACLY	17	A	0.0187	9.40×10−4	0.389	1.11×10−3	9.76×10−5	1.21 (1.10–1.33)	0.898	0.877	0.540
rs4801853	C19orf48	19	C	3.18×10−3	0.0130	0.0744	3.24×10−3	1.13×10−4	1.14 (1.07–1.22)	0.741	0.712	0.634
rs930557	MCPH1	8	G	4.64×10−3	0.395	0.254	0.0279	5.87×10−4	1.15 (1.06–1.24)	0.203	0.181	0.292
rs602662	FUT2	19	C	0.0151	6.95×10−4	0.738	0.0229	1.40×10−3	1.10 (1.04–1.17)	0.493	0.467	0.681
rs2043211	CARD8	19	T	0.1514	0.0592	0.160	0.0311	0.0111	1.09 (1.02–1.16)	0.332	0.314	0.742
rs2066807	STAT2- IL23A	12	C	0.0583	0.0637	0.640	0.107	0.0187	1.16 (1.03–1.31)	0.941	0.931	0.344
rs10489990	CD207	2	A	3.43×10−3	0.0461	0.400	0.460	0.0340	1.07 (1.01–1.14)	0.363	0.347	0.0845
rs2034310	CD300LF	17	T	0.0223	0.0246	0.532	0.197	0.0444	1.09 (1.00–1.18)	0.176	0.166	0.285
rs40401	IL3	5	A	0.153	0.0239	0.465	0.280	0.0827	1.07 (0.99–1.15)	0.223	0.213	0.227
rs2290610	IL5RA	3	A	0.0990	0.0587	0.0369	0.834	0.423	1.03 (0.96–1.09)	0.637	0.634	0.0511
rs379707	FYB	5	T	0.0257	0.169	0.0163	0.458	0.697	1.01 (0.95–1.08)	0.696	0.695	0.00741

Chr = chromosome; RAF = risk allele frequency

Results shown in bold are in the opposite direction to the association identified in the WTCCC nsSNP screen

^aThe WTCCC nsSNP screen included 975 cases and 1466 controls from the UK population

^bReplication Stage 1 includes a total of 1038 cases and 1379 controls from the UK and US population

^cReplication Stage 2 includes a total of 2406 cases and 1216 controls from the Australia, Italy and the UK population

^dThe combined analysis includes all data from the WTCCC nsSNP screen, replication stage 1 and replication stage 2