Table 1.

Association for the AD loci selected for follow-up.

							Discovery meta-analysis		Follow-up datasets		Overall
Chr	Closest gene	SNP	BP	A1	A2	Freq A1	OR [CI 95%]	P	OR [CI 95%]	P	OR [CI 95%]	P
Variants showing novel genome-wide significant association with AD
2	PRKD3/NDUFAF7	rs876461	37515958	A	G	0.143	1.07 [1.04–1.09]	9.14 × 10−7	1.08 [1.04–1.13]	3.07 × 10−4	1.07 [1.05–1.09]	1.34 × 10−9
8	SHARPIN	rs34674752	145154222	A	G	0.052	1.11 [1.06–1.16]	4.02 × 10−6	1.20 [1.10–1.31]	1.65 × 10−5	1.13 [1.09–1.18]	1.00 × 10−9
8	SHARPIN	rs34173062	145158607	A	G	0.085	1.16 [1.11–1.21]	1.33 × 10−11	1.09 [1.02–1.17]	7.35 × 10−3	1.14 [1.10–1.18]	9.62 × 10−13
16	PLCG2	rs3935877	81900853	C	T	0.868	0.92 [0.90–0.95]	1.12 × 10−7	0.92 [0.85–0.99]	1.96 × 10−2	0.92 [0.90–0.95]	6.85 × 10−9
17	CHRNE	rs72835061	4805437	A	C	0.085	1.09 [1.06–1.12]	3.92 × 10−9	1.07 [1.02–1.12]	7.83 × 10−3	1.09 [1.06–1.11]	1.51 × 10−10
21	APP	rs2154481	27473875	C	T	0.483	0.95 [0.93–0.96]	9.26 × 10−10	0.96 [0.93–0.99]	3.31 × 10−3	0.95 [0.94–0.96]	1.39 × 10−11
Previously reported genome-wide significant hits replicating in the follow-up
4	HS3ST1	rs4351014	11027619	C	T	0.684	0.94 [0.92–0.96]	5.37 × 10−10	0.93 [0.88–0.98]	4.54 × 10−3	0.94 [0.92–0.95]	9.16 × 10−12
16	IL34	rs4985556	70694000	A	C	0.111	1.08 [1.05–1.11]	2.28 × 10−8	1.09 [1.03–1.16]	4.59 × 10−3	1.08 [1.06–1.11]	3.91 × 10−10
16	PLCG2	rs12444183	81773209	A	G	0.407	0.95 [0.93–0.97]	1.48 × 10−8	0.92 [0.88–0.96]	3.23 × 10−5	0.95 [0.93–0.96]	6.81 × 10−12
Suggestive signals (not replicating)
14	ELK2AP	rs7153315	106195719	C	G	0.750	0.94 [0.92–0.96]	9.80 × 10−8	1.16 [1.01–1.33]	0.0412	0.94 [0.92–0.97]	9.04 × 10−7
15	SPPL2A	rs76523702	51002342	C	T	0.802	1.06 [1.04–1.08]	6.86 × 10−8	1.02 [0.97–1.07]	0.3501	1.05 [1.03–1.08]	1.08 × 10−7

Results obtained with a fixed effects inverse-variance-weighted meta-analysis on the discovery and follow-up stages. Freq A1 is from GR@ACE discovery dataset. P value for significance <5 × 10⁻⁸. Effect allele: A1.