Table 1.

APOE variants and the 31 SNPs and, their closest genes, log hazard ratio estimates used for PHS construction in Desikan et al.10 and their odds ratio estimates as in Lambert et al.6

SNP	Chr	Position	Gene	Β = log(HR) Desikan et al. (2017)	−log10(P‐value) Desikan et al. (2017)	B = log(OR) in IGAP	B = log(OR) IGAP_ noGERAD	A1 IGAP_ noGERAD
APOE ε2	19		APOE	−0.47	>15.0	−0.66 1	−0.492	ε2
APOE ε4	19		APOE	1.03	>20.0	1.12 2	0.662	ε4
rs4266886	1	207685786	CR1	−0.09	2.7	−0.1542	0.1520	T
rs61822977	1	207796065	CR1	−0.08	2.8	−0.0805	−0.0820	A
rs6733839	2	127892810	BIN1	−0.15	10.5	−0.1880	0.1807	T
rs10202748	2	234003117	INPP5D	−0.06	2.1	−0.058	−0.0603	A
rs115124923	6	32510482	HLA‐DRB5	0.17	7.4	0.1216	−0.0973	A
rs115675626	6	32669833	HLA‐DQB1	−0.11	3.2	−0.1246	0.1040	A
rs1109581	6	47678182	GPR115	−0.07	2.6	−0.0651	0.0601	T
rs17265593	7	37619922	BC043356	−0.23	3.6	−0.0659	−0.0620	T
rs2597283	7	37690507	BC043356	0.28	4.7	0.0679	0.0629	A
rs1476679	7	100004446	ZCWPW1	0.11	4.9	0.1741	0.0712	T
rs78571833	7	143122924	AL833583	0.14	3.8	0.0795	0.2083	A
rs12679874	8	27230819	PTK2B	−0.09	4.2	−0.0795	−0.0748	A
rs2741342	8	27330096	CHRNA2	0.09	2.9	0.0916	−0.0872	T
rs7831810	8	27430506	CLU	0.09	3.0	0.083	−0.0774	A
rs1532277	8	27466181	CLU	0.21	8.3	0.1385	−0.1271	T
rs9331888	8	27468862	CLU	0.16	5.1	0.0819	−0.0806	C
rs7920721	10	11720308	CR595071	−0.07	2.9	−0.0713	−0.0660	A
rs3740688	11	47380340	SPI1	0.07	2.8	0.0724	0.0739	T
rs7116190	11	59964992	MS4A6A	0.08	3.9	0.0991	−0.0968	A
rs526904	11	85811364	PICALM	−0.20	2.3	−0.1188	−0.1130	T
rs543293	11	85820077	PICALM	0.30	4.2	0.1257	−0.1192	A
rs11218343	11	121435587	SORL1	0.18	2.8	0.2697	0.2539	T
rs6572869	14	53353454	FERMT2	−0.11	3.0	−0.0947	0.1006	A
rs12590273	14	92934120	SLC24A4	0.10	3.5	0.1348	0.1231	T
rs7145100	14	107160690	abParts	0.08	2.0	0.1047	−0.1081	C
rs74615166	15	64725490	TRIP4	−0.23	3.1	−0.3358	−0.2986	T
rs2526378	17	56404349	BZRAP1	0.09	4.9	0.0762	0.0754	A
rs117481827	19	1021627	C19orf6	−0.09	2.5	−0.1288	−0.1059	T
rs7408475	19	1050130	ABCA7	0.18	4.3	0.0971	−0.0973	C
rs3752246	19	1056492	ABCA7	−0.25	8.4	−0.1345	−0.1308	C
rs7274581	20	55018260	CASS4	0.10	2.1	0.139	0.1497	A

First 6th columns are the same as they were presented in Desikan et al. (2017),10 followed by effect sizes from IGAP and IGAP_noGERAD summary statistics and reference allele as it was presented in IGAP.

¹ B estimated on GERAD data when running LR.

² B estimated on GERAD data when running Cox regression.