Table 2.

summary of stage 1, stage 2 and overall meta-analyses for sNPs reaching genome-wide significance after stages 1 and 2

						Stage 1		Stage 2		Overall
SNPa	Chr.	Positionb	Closest genec	Major/minor alleles	MAFd	OR (95% CI)e	Meta P value	OR (95% CI)e	Meta P value	OR (95% CI)e	Meta P value	I2 (%), P valuef
Known GWAS-defined associated genes
rs6656401	1	207692049	CR1	G/A	0.197	1.17 (1.12–1.22)	7.7 × 10−15	1.21 (1.14–1.28)	7.9 × 10−11	1.18 (1.14–1.22)	5.7 × 10−24	0, 7.8 × 10−1
rs6733839	2	127892810	BIN1	C/T	0.409	1.21 (1.17–1.25)	1.7 × 10−26	1.24 (1.18–1.29)	3.4 × 10−19	1.22 (1.18–1.25)	6.9 × 10−44	28, 6.1 × 10−2
rs10948363	6	47487762	CD2AP	A/G	0.266	1.10 (1.07–1.14)	3.1 × 10−8	1.09 (1.04–1.15)	4.1 × 10−4	1.10 (1.07–1.13)	5.2 × 10−11	0, 9 × 10−1
rs11771145	7	143110762	EPHA1	G/A	0.338	0.90 (0.87–0.93)	8.8 × 10−10	0.90 (0.86–0.95)	2.8 × 10−5	0.90 (0.88–0.93)	1.1 × 10−13	14, 2.4 × 10−1
rs9331896	8	27467686	CLU	T/C	0.379	0.86 (0.84–0.89)	9.6 × 10−17	0.86 (0.82–0.90)	4.5 × 10−10	0.86 (0.84–0.89)	2.8 × 10−25	0, 4.9 × 10−1
rs983392	11	59923508	MS4A6A	A/G	0.403	0.90 (0.87–0.93)	2.8 × 10−11	0.90 (0.86–0.94)	4.5 × 10−6	0.90 (0.87–0.92)	6.1 × 10−16	1, 4.5 × 10−1
rs10792832	11	85867875	PICALM	G/A	0.358	0.88 (0.85–0.91)	6.5 × 10−16	0.85 (0.81–0.89)	1.1 × 10−11	0.87 (0.85–0.89)	9.3 × 10−26	0, 9.8 × 10−1
rs4147929	19	1063443	ABCA7	G/A	0.190	1.14 (1.10–1.20)	1.7 × 10−9	1.17 (1.10–1.24)	9.9 × 10−8	1.15 (1.11–1.19)	1.1 × 10−15	0, 9.4 × 10−1
rs3865444g	19	51727962	CD33	C/A	0.307	0.91 (0.88–0.94)	5.1 × 10−8	0.99 (0.94–1.04)	6.9 × 10−1	0.94 (0.91–0.96)	3.0 × 10−6	0, 6.9 × 10−1
New loci reaching genome-wide significance in the discovery analysis
rs9271192	6	32578530	HLA-DRB5– HLA-DRB1	A/C	0.276	1.11 (1.07–1.16)	1.6 × 10−8	1.12 (1.06–1.18)	4.2 × 10−5	1.11 (1.08–1.15)	2.9 × 10−12	0, 5.4 × 10−1
rs28834970	8	27195121	PTK2B	T/C	0.366	1.10 (1.07–1.14)	3.3 × 10−9	1.11 (1.06–1.17)	4.3 × 10−6	1.10 (1.08–1.13)	7.4 × 10−14	10, 3.0 × 10−1
rs11218343	11	121435587	SORL1	T/C	0.039	0.76 (0.70–0.83)	5.0 × 10−11	0.78 (0.70–0.88)	4.0 × 10−5	0.77 (0.72–0.82)	9.7 × 10−15	0, 8.3 × 10−1
rs10498633	14	92926952	SLC24A4 RIN3	G/T	0.217	0.90 (0.87–0.94)	1.5 × 10−7	0.93 (0.88–0.98)	7.8 × 10−3	0.91 (0.88–0.94)	5.5 × 10−9	0, 6.3 × 10−1
rs8093731g	18	29088958	DSG2	C/T	0.017	0.54 (0.43–0.67)	4.6 × 10−8	1.01 (0.80–1.28)	9.0 × 10−1	0.73 (0.62–0.86)	1.0 × 10−4	38, 3.9 × 10−2
New loci reaching genome-wide significance in the combined discovery and replication analysis
rs35349669	2	234068476	INPP5D	C/T	0.488	1.07 (1.03–1.10)	9.6 × 10−5	1.10 (1.05–1.15)	5.7 × 10−5	1.08 (1.05–1.11)	3.2 × 10−8	0, 8.0 × 10−1
rs190982	5	88223420	MEF2C	A/G	0.408	0.92 (0.89–0.95)	2.5 × 10−6	0.93 (0.89–0.98)	3.4 × 10−3	0.93 (0.90–0.95)	3.2 × 10−8	0, 6.4 × 10−1
rs2718058	7	37841534	NME8	A/G	0.373	0.93 (0.90–0.96)	1.3 × 10−5	0.91 (0.87–0.95)	6.3 × 10−5	0.93 (0.90–0.95)	4.8 × 10−9	0, 9.2 × 10−1
rs1476679	7	100004446	ZCWPW1	T/C	0.287	0.92 (0.89–0.96)	7.4 × 10−6	0.89 (0.85–0.94)	9.7 × 10−6	0.91 (0.89–0.94)	5.6 × 10−10	0, 7.0 × 10−1
rs10838725	11	47557871	CELF1	T/C	0.316	1.08 (1.04–1.11)	6.7 × 10−6	1.09 (1.04–1.14)	4.1 × 10−4	1.08 (1.05–1.11)	1.1 × 10−8	0, 7.6 × 10−1
rs17125944	14	53400629	FERMT2	T/C	0.092	1.13 (1.07–1.19)	1.0 × 10−5	1.17 (1.08–1.26)	1.6 × 10−4	1.14 (1.09–1.19)	7.9 × 10−9	10, 3.0 × 10−1
rs7274581	20	55018260	CASS4	T/C	0.083	0.87 (0.82–0.92)	1.6 × 10−6	0.89 (0.82–0.96)	4.1 × 10−3	0.88 (0.84–0.92)	2.5 × 10−8	0, 9.9 × 10−1

Chr., chromosome.

^aSNPs showing the best level of association after meta-analysis of stages 1 and 2.

^bBuild 37, assembly hg19.

^cGenes located ± 100 kb of the top SNP.

^dAverage in the discovery sample.

^eCalculated with respect to the minor allele.

^fCochran’s Q test.

^gNot replicated in stage 2.