Table 1. Seven SNPs in APOE and TOMM40 (indicated by * of the SNP IDs) and 29 novel SNPs reaching exome-wide significance (p < 3.0 x 10⁻⁷, Bonferroni-corrected cutoff of p < 0.05 / # tests): Population minor allele frequency (MAF) in cases and controls, MAF in controls processed by Illumina or NimbleGen exome capture kit, and MAF in Non-Finish European (NFE) cohort of the ExAC database (http://exac.broadinstitute.org/).

Chr	Position	Ref	Alt	p-value (Model 1)	p-value (Model 2)	Gene	SNP ID	ADSP Cases MAF	ADSP Controls MAF	ADSP Controls MAF, Illumina	ADSP Controls MAF, NimbleGen	ExAC AAF, NFE
19	45411941	T	C	2.4E-185	N/A	APOE	rs429358*	0.2293	0.0701	0.074	0.067	0.1504
19	45396144	C	T	4.7E-103	0.7097	TOMM40	rs11556505*	0.2023	0.0879	0.085	0.090	0.0875
19	45395714	T	C	2.4E-75	0.1439	TOMM40	rs157581*	0.2766	0.1629	0.165	0.162	0.2326
19	45412079	C	T	1.8E-48	N/A	APOE	rs7412*	0.042	0.0988	0.116	0.087	0.0813
15	75913319	T	G	4.3E-45	2.7E-35	SNUPN	rs1004285543	0.0825	0.0255	0.063	0.001	NA
17	25973604	A	C	2.6E-45	1.4E-34	LGALS9	rs761436847	0.0823	0.0256	0.056	0.006	0.0906
6	36979483	T	G	1.7E-39	1.6E-29	FGD2	rs769719224	0.0998	0.0404	0.072	0.019	0.0294
14	99976645	A	C	4.1E-36	7.5E-28	CCNK	rs745936510	0.0899	0.0348	0.068	0.013	0.0713
13	114188430	C	T	4.7E-38	2.2E-27	TMCO3	rs77834374	0.1068	0.0459	0.080	0.024	0.1336
14	99976639	G	C	9.4E-36	3.7E-26	CCNK	rs778243462	0.0932	0.0372	0.071	0.015	0.0808
17	25973598	A	C	4.3E-25	1.1E-21	LGALS9	rs760143837	0.0472	0.014	0.033	0.002	0.0243
14	77706020	A	C	9.7E-28	6.3E-21	TMEM63C	rs774212969	0.0577	0.019	0.036	0.008	0.009
19	45397229	G	A	9.6E-21	0.3137	TOMM40	rs1160983*	0.0173	0.0416	0.045	0.039	0.0718
11	117280516	A	C	7.9E-29	2.5E-20	CEP164	rs756182128	0.0748	0.0296	0.050	0.016	0.081
3	42739737	T	G	5.7E-25	9.7E-20	HHATL	rs763168412	0.0539	0.0182	0.034	0.008	0.0919
3	48451952	A	C	3.2E-24	2.7E-19	PLXNB1	rs770786389	0.0562	0.02	0.037	0.009	0.0255
19	45397307	C	T	1.5E-18	0.928	TOMM40	rs112849259*	0.0308	0.0107	0.005	0.014	0.0011
12	56622883	A	C	4.3E-24	1.2E-17	NABP2	rs757798976	0.0714	0.0301	0.054	0.014	0.0476
2	85662149	A	C	4.0E-21	4.3E-16	SH2D6	rs748669078	0.068	0.0309	0.044	0.022	0.0026
19	10946797	G	C	6.4E-21	2.5E-15	TMED1	rs767166604	0.0421	0.0128	0.029	0.002	0.0007
14	105932775	G	C	5.5E-21	3.1E-15	MTA1	rs782227993	0.0627	0.0259	0.047	0.012	0.0208
6	29429950	A	C	1.1E-19	3.6E-15	OR2H1	rs746691570	0.0402	0.0132	0.022	0.007	0.0207
11	117280522	A	C	6.5E-21	3.3E-14	CEP164	rs758240656	0.0529	0.0198	0.037	0.009	0.0768
2	85662154	A	C	4.9E-18	4.0E-14	SH2D6	rs760146451	0.0617	0.0288	0.040	0.021	0.0018
13	88330245	A	C	3.1E-17	1.1E-13	SLITRK5	rs773717935	0.0277	0.0065	0.014	0.002	3.1E-05
19	45409167	C	G	9.7E-13	0.3854	APOE	rs440446*	0.3332	0.3817	0.361	0.395	0.4346
19	10946802	T	C	1.2E-16	3.1E-12	TMED1	rs776909029	0.0366	0.0117	0.028	0.001	0.0009
9	34564740	A	C	6.5E-16	3.6E-12	CNTFR	rs774039930	0.0516	0.0222	0.039	0.011	0.0008
3	108474687	T	G	1.4E-15	5.8E-12	RETNLB	rs199707443	0.0328	0.0107	0.025	0.001	0.0493
19	43025485	T	G	2.6E-15	7.7E-12	CEACAM1	rs763190977	0.0921	0.0523	0.107	0.016	0.0026
3	31659462	A	T	4.8E-17	9.2E-12	STT3B	rs74346226	0.0891	0.0514	0.076	0.035	0.131
12	109719316	T	G	9.1E-12	2.1E-10	FOXN4	rs760573591	0.0309	0.0115	0.025	0.003	1.5E-05
8	145112936	T	C	6.8E-14	5.0E-10	OPLAH	rs781948612	0.0331	0.0114	0.026	0.002	0.0364
19	42799299	T	C	5.7E-12	1.4E-09	CIC	rs745695673	0.019	0.0043	0.011	0.000	0
13	111164389	A	C	7.2E-12	1.6E-08	COL4A2	rs199702442	0.0517	0.0274	0.041	0.018	0.0285
22	30951295	T	G	2.0E-11	1.8E-08	GAL3ST1	rs762634521	0.0204	0.0056	0.013	0.001	0.028

Model 1 adjusted for sequencing center and the first four PCs underlying population substructure. Model 2 adjusted for sequencing center, the first 4 PCs, sex and APOE genotype.