Table 2 Summary of association results in the stage I and stage II analysis for new loci at the time of analysis with a genome-wide significant signal

From: New insights into the genetic etiology of Alzheimer’s disease and related dementias

Locus number	Variant^a	Chromosome	Position^b	Gene^c	Minor/major allele	MAF^d	OR^e	95% CI	P value
1	rs141749679	1	109345810	SORT1	C/T	0.004	1.38	1.24–1.54	7.5 × 10⁻⁹
2	rs72777026	2	9558882	ADAM17	G/A	0.144	1.06	1.04–1.08	2.7 × 10⁻⁸
3	rs17020490	2	37304796	PRKD3	C/T	0.145	1.06	1.04–1.08	3.3 × 10⁻⁹
4	rs143080277	2	105749599	NCK2	C/T	0.005	1.47	1.33–1.63	2.1 × 10⁻¹³
5	rs139643391	2	202878716	WDR12	T/TC	0.131	0.94	0.92–0.96	1.1 × 10⁻⁸
6	rs16824536	3	155069722	MME	A/G	0.054	0.92	0.89–0.95	3.6 × 10⁻⁸
6	rs61762319	3	155084189	MME	G/A	0.026	1.16	1.11–1.21	2.2 × 10⁻¹¹
7	rs3822030	4	993555	IDUA	G/T	0.429	0.95	0.94–0.96	8.3 × 10⁻¹²
8	rs2245466	4	40197226	RHOH	G/C	0.343	1.05	1.03–1.06	1.2 × 10⁻⁹
9	rs112403360	5	14724304	ANKH	A/T	0.073	1.09	1.06–1.12	2.3 × 10⁻⁹
10	rs62374257	5	86927378	COX7C	C/T	0.23	1.07	1.05–1.09	1.4 × 10⁻¹⁵
11	rs871269	5	151052827	TNIP1	T/C	0.326	0.96	0.95–0.97	8.7 × 10⁻⁹
12	rs113706587	5	180201150	RASGEF1C	A/G	0.11	1.09	1.07–1.12	2.2 × 10⁻¹⁶
13	rs785129	6	114291731	HS3ST5	T/C	0.35	1.04	1.03–1.06	2.4 × 10⁻⁹
14	rs6943429	7	7817263	UMAD1	T/C	0.42	1.05	1.03–1.06	1.0 × 10⁻¹⁰
15	rs10952097	7	8204382	ICA1	T/C	0.114	1.07	1.05–1.10	6.8 × 10⁻⁹
16	rs13237518	7	12229967	TMEM106B	A/C	0.411	0.96	0.94–0.97	4.9 × 10⁻¹¹
17	rs1160871	7	28129126	JAZF1	G/GTCTT	0.222	0.95	0.93–0.97	9.8 × 10⁻⁹
18	rs76928645	7	54873635	SEC61G	T/C	0.103	0.93	0.91–0.95	1.6 × 10⁻¹⁰
19	rs1065712	8	11844613	CTSB	C/G	0.053	1.09	1.06–1.12	1.9 × 10⁻⁹
20	rs34173062	8	144103704	SHARPIN	A/G	0.081	1.13	1.09–1.16	1.7 × 10⁻¹⁶
21	rs1800978	9	104903697	ABCA1	G/C	0.13	1.06	1.04–1.08	1.6 × 10⁻⁹
22	rs7068231	10	60025170	ANK3	T/G	0.403	0.95	0.94–0.96	3.3 × 10⁻¹³
23	rs6586028	10	80494228	TSPAN14	C/T	0.196	0.93	0.91–0.94	2.0 × 10⁻¹⁹
24	rs6584063	10	96266650	BLNK	G/A	0.043	0.89	0.86–0.92	6.7 × 10⁻¹¹
25	rs7908662	10	122413396	PLEKHA1	G/A	0.467	0.96	0.95–0.97	2.6 × 10⁻⁹
26	rs6489896	12	113281983	TPCN1	C/T	0.076	1.08	1.05–1.10	1.8 × 10⁻⁹
27	rs7157106	14	105761758	IGH gene cluster	A/G	0.36	1.05	1.03–1.07	2.0 × 10⁻⁸
27	rs10131280	14	106665591	IGH gene cluster	A/G	0.133	0.94	0.92–0.96	4.3 × 10⁻¹⁰
28	rs3848143	15	64131307	SNX1	G/A	0.22	1.05	1.04–1.07	8.4 × 10⁻¹¹
29	rs12592898	15	78936857	CTSH	A/G	0.133	0.94	0.92–0.96	4.2 × 10⁻⁹
30	rs1140239	16	30010081	DOC2A	T/C	0.379	0.94	0.93–0.96	2.6 × 10⁻¹³
31	rs450674	16	79574511	MAF	C/T	0.373	0.96	0.95–0.98	3.2 × 10⁻⁸
32	rs16941239	16	86420604	FOXF1	A/T	0.029	1.13	1.08–1.17	1.3 × 10⁻⁸
33	rs56407236	16	90103687	PRDM7	A/G	0.069	1.11	1.08–1.14	6.5 × 10⁻¹⁵
34	rs35048651	17	1728046	WDR81	T/TGAG	0.214	1.06	1.04–1.08	7.7 × 10⁻¹¹
35	rs2242595	17	18156140	MYO15A	A/G	0.112	0.94	0.92–0.96	1.1 × 10⁻⁹
36	rs5848	17	44352876	GRN	T/C	0.289	1.07	1.06–1.09	2.4 × 10⁻²⁰
37	rs149080927	19	1854254	KLF16	G/GC	0.48	1.05	1.04–1.07	5.1 × 10⁻¹⁰
38	rs9304690	19	49950060	SIGLEC11	T/C	0.24	1.05	1.03–1.07	4.7 × 10⁻⁹
39	rs587709	19	54267597	LILRB2	C/T	0.325	1.05	1.04–1.07	3.6 × 10⁻¹¹
40	rs1358782	20	413334	RBCK1	A/G	0.246	0.95	0.94–0.97	1.6 × 10⁻⁸
41	rs6742	20	63743088	SLC2A4RG	T/C	0.221	0.95	0.93–0.97	2.6 × 10⁻⁹
42	rs2154481	21	26101558	APP	C/T	0.476	0.95	0.94–0.97	1.0 × 10⁻¹²

P values are two-sided raw P values derived from a fixed-effect meta-analysis.
^ars number, according to dbSNP build 153.
^bGRCh38 assembly.
^cNearest protein-coding gene according to GENCODE release 33.
^dWeighted average MAF across all discovery studies.
^eApproximate OR calculated with respect to the minor allele.

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Table 2 Summary of association results in the stage I and stage II analysis for new loci at the time of analysis with a genome-wide significant signal

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