Table 2.

Association statistics of the 29 tested AD-associated variants

Chr	Position	Rs ID	Gene	A1	$\log {\mathrm{OR}}_{\mathrm{l}}^{\mathrm{k}}$(SE)	$\log {\mathrm{OR}}_{\mathrm{EA}-\mathrm{EC}}^{\mathrm{k}}$(SE)	P valueEA–EC	${\mathrm{E}}_{\mathrm{EA}-\mathrm{EC}}^{\mathrm{k}}$ (95% CI, p)	AFEA	AFNC	AFEC
6	41,129,252	rs75932628	TREM2 (R47H)	T	0.89 (0.09)	5.75 (5.13)	2.63 × 10−1	6.46 (− 4.83–18.46, 3.5×10−1)	0.003	0.001	0.000
10	11,720,308	rs7920721	ECHDC3	G	0.07 (0.01)	0.31 (0.10)	2.93 × 10−3 *	4.56 (1.55–8.93, 1.8 × 10−2)	0.430	0.389	0.357
14	92,926,952	rs10498633	SLC24A4-RIN3	T	− 0.09 (0.01)	− 0.42 (0.11)	1.30 × 10−4 *	4.50 (2.08– 7.93, 2.8 × 10−3)	0.206	0.236	0.292
7	37,841,534	rs2718058	NME8	G	− 0.08 (0.01)	− 0.29 (0.10)	3.72 × 10−3 *	3.80 (1.17– 7.28, 3.3 × 10−2)	0.360	0.367	0.433
16	81,942,028	rs72824905	PLCG2	G	− 0.39 (0.06)	− 1.27 (0.40)	1.38 × 10−3 *	3.28 (1.26–5.98, 2.8×10−2)	0.008	0.012	0.025
6	32,578,530	rs9271192	HLA-DRB1	A	− 0.11 (0.01)	− 0.35 (0.16)	3.06 × 10−2 *	3.20 (0.35–6.65, 1.3 × 10−1)	0.712	0.727	0.780
7	100,004,446	rs1476679	ZCWPW1	T	0.09 (0.01)	0.26 (0.11)	1.34 × 10−2 *	2.97 (0.60−6.10, 1.0 × 10−1)	0.703	0.674	0.649
19	1,063,443	rs4147929	ABCA7 (A>G)	G	− 0.14 (0.02)	− 0.32 (0.14)	2.11 × 10−2 *	2.26 (0.30–4.42, 2.2 × 10−1)	0.809	0.834	0.855
19	45,412,079	rs7412	APOE (ε2)	T	− 0.79 (0.03)	− 1.76 (0.18)	3.16 × 10−21 *	2.24 (1.75–2.77, 1.4 × 10−7)	0.033	0.091	0.149
4	11,711,232	rs13113697	HS3ST1	G	− 0.07 (0.01)	− 0.14 (0.12)	2.41 × 10−1	2.06 (− 1.49–6.13, 5.4×10−1)	0.265	0.268	0.247
17	47,297,297	rs616338	ABI3	C	− 0.36 (0.05)	− 0.74 (0.57)	1.93 × 10−1	2.06 (− 0.99–5.59, 5.2 × 10−1)	0.017	0.009	0.006
6	47,487,762	rs10948363	CD2AP	G	0.10 (0.01)	0.19 (0.11)	8.84 × 10−2	2.00 (− 0.34–4.60, 4.1×10−1)	0.284	0.272	0.245
19	45,411,941	rs429358	APOE (ε4)	C	1.05 (0.03)	2.08 (0.17)	1.31 × 10−33 *	1.99 (1.65–2.33, 1.5 × 10−9)	0.429	0.166	0.082
7	143,110,762	rs11771145	EPHA1	A	− 0.10 (0.01)	− 0.20 (0.10)	5.96 × 10−2	1.94 (− 0.09–4.29, 3.7 × 10−1)	0.325	0.345	0.371
11	47,557,871	rs10838725	CELF1	C	0.08 (0.01)	0.14 (0.11)	2.05 × 10−1	1.78 (− 0.95–5.11, 5.8 × 10−1)	0.328	0.314	0.302
8	27,195,121	rs28834970	PTK2B	C	0.10 (0.01)	0.18 (0.10)	8.96 × 10−2	1.76 (− 0.23–4.09, 4.7×10−1)	0.395	0.376	0.353
11	59,923,508	rs983392	MS4A6A	G	− 0.11 (0.01)	− 0.17 (0.10)	9.39 × 10−2	1.56 (− 0.20–3.61, 5.4 × 10−1)	0.397	0.403	0.439
11	121,435,587	rs11218343	SORL1	C	− 0.26 (0.03)	− 0.39 (0.25)	1.21 × 10−1	1.48 (− 0.39–3.51, 6.2 × 10−1)	0.033	0.040	0.047
2	127,892,810	rs6733839	BIN1	T	0.20 (0.01)	0.25 (0.10)	1.12 × 10−2 *	1.28 (0.31–2.29, 5.8 × 10−1)	0.456	0.413	0.390
11	85,867,875	rs10792832	PICALM	G	0.14 (0.01)	0.15 (0.10)	1.26 × 10−1	1.09 (− 0.30–2.56, 9.1 × 10−1)	0.653	0.614	0.612
20	55,018,260	rs7274581	CASS4	C	− 0.13 (0.02)	− 0.14 (0.18)	4.41 × 10−1	1.06 (−1.83–4.07, 9.7 × 10−1)	0.075	0.088	0.084
6	41,129,207	rs143332484	TREM2 (R62H)	T	0.50 (0.07)	0.48 (0.48)	3.21 × 10−1	0.97 (− 0.96–3.09, 9.8 × 10−1)	0.017	0.015	0.009
17	44,353,222	rs118172952	KANSL1	G	− 0.14 (0.03)	− 0.13 (0.14)	3.44 × 10−1	0.97 (−1.08−3.64, 9.6 × 10−1)	0.191	0.202	0.221
1	207,692,049	rs6656401	CR1	G	− 0.17 (0.01)	− 0.12 (0.12)	3.11 × 10−1	0.75 (− 0.75–2.21, 7.4 × 10−1)	0.781	0.803	0.806
19	1,061,892	rs200538373	ABCA7 (G>C)	C	− 0.65 (0.14)	− 0.44 (0.80)	5.81 × 10−1	0.68 (− 1.83–3.54, 7.9 × 10−1)	0.004	0.004	0.006
8	27,467,686	rs9331896	CLU	T	0.15 (0.01)	0.09 (0.10)	3.99 × 10−1	0.60 (− 0.78–2.06, 5.8 × 10−1)	0.361	0.400	0.378
2	234,068,476	rs35349669	INPP5D	T	0.08 (0.01)	0.03 (0.10)	7.83 × 10−1	0.36 (− 2.33–3.16, 6.2 × 10−1)	0.474	0.496	0.486
14	53,400,629	rs17125944	FERMT2	C	0.13 (0.02)	− 0.11 (0.16)	4.99 × 10−1	− 0.82 (− 3.46–1.60, 1.3×10−1)	0.104	0.105	0.114
5	88,223,420	rs190982	MEF2C	A	0.08 (0.01)	− 0.14 (0.10)	1.70 × 10−1	− 1.86 (− 5.01–0.77, 3.3 × 10−2)	0.408	0.406	0.372
Average								1.90 ± 0.29, p = 9.0 x 10−4

Chr, chromosome; Position, chromosomal position (GRCh37); Rs ID, variant ID; Gene, gene associated with the variant according to paper in which the variant was found; A1, tested allele (alternative allele according to Haplotype Reference Consortium (HRC) panel); $logO{R}_l^k$(SE), log(odds ratio) and relative standard error for variant k reported by study with largest sample size; $logO{R}_{EA-EC}^k$ (SE), log(odds ratio) and relative standard error in extreme control association; P value, p value of AD association of extreme AD cases vs centenarian controls; $E_{EA-EC}^k$ (95% CI, p), change in effect size, 95% confidence intervals and p value of difference when using extreme phenotypes relative to published effect sizes; AF_EA , tested allele frequency in AD extreme cases; AF_NC, tested allele frequency in normal controls; AF_EC, tested allele frequency in centenarian controls. Bold: variants for which the E^k_EA-EC was significantly different from published effect size; *: significant at p < 0.05