Table 2 |.

Summary of discovery Stage 1, Stage 2, Stage 3 (A and B), and overall meta-analysis results of potential novel loci

Stage 3A						Stage 1 + 2 (n = 82,771)			Stage 3A (n = 11,666)			Overall (n = 94,437)
SNPa	Chr.	Positionb	Closest genec	Major/ minor allele	MAFe	OR	95% CIf	P	OR	95% CIf	P	OR	95% CIf	Meta P
rs4735340	8	95976251	NDUFAF6	T/A	0.476	0.94	0.92–0.96	3.4 × 10−7	0.92	0.83–1.02	9.7 × 10−2	0.94	0.92–0.96	9.2 × 10−8
rs7920721g	10	11720308	ECHDC3	A/G	0.390	1.08	1.05–1.11	2.3 × 10−9	1.11	1.04–1.18	1.5 × 10−3	1.08	1.06–1.11	1.8 × 10−11
rs7295246	12	43967677	ADAMTS20	T/G	0.413	1.07	1.04–1.09	2.7 × 10−7	1.02	0.96–1.09	4.5 × 10−1	1.06	1.04–1.08	3.9 × 10−7
rs10467994	15	51008687	SPPL2A	T/C	0.333	0.94	0.91–0.96	3.9 × 10−7	0.97	0.87–1.08	6.2 × 10−1	0.94	0.92–0.96	4.3 × 10−7
rs593742	15	59045774	ADAM10	A/G	0.295	0.93	0.91–0.96	1.3 × 10−7	0.91	0.85–0.98	1.5 × 10−2	0.93	0.91–0.95	6.8 × 10−9
rs7185636	16	19808163	IQCK	T/C	0.180	0.92	0.89–0.95	8.4 × 10−8	0.94	0.86–1.01	1.1 × 10−1	0.92	0.89–0.95	2.4 × 10−8
rs2632516	17	56409089	MIR142/TSPOAP1-AS1d	G/C	0.440	0.94	0.92–0.96	2.3 × 10−7	0.91	0.82–1.01	7.5 × 10−2	0.94	0.91–0.96	5.3 × 10−8
rs138190086	17	61538148	ACE	G/A	0.020	1.32	1.20–1.45	7.5 × 10−9	1.17	0.92–1.48	2.1 × 10−1	1.30	1.19–1.42	5.3 × 10−9
rs2830500	21	28156856	ADAMTS1	C/A	0.308	0.93	0.91–0.96	7.4 × 10−8	0.95	0.89–1.02	1.3 × 10−1	0.93	0.91–0.96	2.6 × 10−8
Stage 3B						Stage 1 (n = 63,926)			Stage 3B (n = 30,511)h			Overall (n = 94,437)h
SNPa	Chr.	Positionb	Closest genec	Major/ minor allele	MAFe	OR	95% CIf	P	OR	95% CIf	P	OR	95% CIf	Meta P
rs71618613	5	29005985	SUCLG2P4	A/C	0.010	0.68	0.57–0.80	9.8 × 10−6	0.76	0.63–0.93	6.8 × 10−3	0.71	0.63–0.81	3.3 × 10−7
rs35868327	5	52665230	FST T/A	A/C	0.013	0.69	0.59–0.80	7.8 × 10−7	0.58	0.29–1.17	1.2 × 10−1	0.68	0.59–0.79	2.6 × 10−7
rs114812713	6	41034000	OARD1	G/C	0.030	1.35	1.24–1.47	4.5 × 10−12	1.23	1.06–1.42	7.2 × 10−3	1.32	1.22–1.42	2.1 × 10−13
rs62039712	16	79355857	WWOX	G/A	0.116	1.17	1.10–1.23	1.2 × 10−7	1.14	0.96–1.36	1.3 × 10−1	1.16	1.10–1.23	3.7 × 10−8

Novel loci were defined as loci not reported in Lambert et al.¹ with (1) a Stage 1 + 2 meta P < 5 × 10⁻⁷ (nine variants after excluding TREM2) (Stage 3A) or (2) a MAF < 0.05 and Stage 1 P < 1 × 10⁻⁵ or MAF ≥ 0.05 and Stage 1 P < 5 × 10⁻⁶ for genome regions not covered on the Stage 2 custom array (Stage 3B).

^aSNPs showing the best level of association after meta-analysis of Stages 1, 2 and 3.

^bBuild 37, assembly hg19.

^cBased on position of top SNP in reference to the RefSeq assembly.

^dVariant is annotated to both gene features.

^eAverage in the discovery sample.

^fCalculated with respect to the minor allele.

^gRecently identified as a LOAD locus in two separate 2017 studies.

^hSample sizes for these loci are smaller (overall n = 89,769 for SUCLG2P4, 65,230 for FST, and n = 69,898 for WWOX).