Table 3. Discovery analysis: SNP association with ALS outcome using GENEVA+WTCCC2 controls.

						Minor allele frequency
Chr	SNP	Pos (build 36)	Closest gene (distance)	Odds ratio (95% CI)	P	Cases	GENEVA controls	WTCCC2 controls
13	rs9534003	44375190	NUFIP1 (36 kb)	1.7 (1.4, 2.1)	1.3E-06	0.18	0.12	0.12
15	rs11071021	52143583	UNC13C	0.7 (0.6, 0.8)	1.9E-06	0.36	0.47	0.42
20	rs6080544	16987959	PCSK2 (167 kb)	0.7 (0.6, 0.8)	2.6E-06	0.33	0.42	0.39
5	rs7707833	74323619	GCNT4 (35 kb)	0.7 (0.6, 0.8)	2.8E-06	0.33	0.40	0.39
20	rs6075164	16985876	PCSK2 (169 kb)	0.7 (0.6, 0.8)	2.8E-06	0.33	0.43	0.39
20	rs6075165	16986263	PCSK2 (168 kb)	0.7 (0.6, 0.8)	3.8E-06	0.33	0.43	0.39
2	rs6746842	118523065	CCDC93 (35 kb)	1.5 (1.2, 1.7)	4.0E-06	0.35	0.27	0.29
2	rs7571323	118549038	INSIG2 (13 kb)	1.5 (1.2, 1.7)	4.1E-06	0.35	0.27	0.29
2	rs2276695	118531338	INSIG2 (31 kb)	1.4 (1.2, 1.7)	4.2E-06	0.45	0.37	0.38
2	rs11688631	119296905	EN1 (19 kb)	1.5 (1.2, 1.7)	4.5E-06	0.49	0.42	0.45
14	rs6574039	71560768	RGS6	0.6 (0.5, 0.7)	5.1E-06	0.14	0.21	0.18
18	rs639964	40708686	SETBP1	0.7 (0.6, 0.8)	5.2E-06	0.38	0.46	0.44
16	rs12929572	60610083	CDH8	0.7 (0.6, 0.8)	5.2E-06	0.28	0.37	0.35
18	rs617459	40707045	SETBP1	0.7 (0.6, 0.8)	5.5E-06	0.38	0.46	0.44
3	rs2703029	54878655	CACNA2D3	1.4 (1.2, 1.7)	5.8E-06	0.48	0.43	0.45
18	rs7242525	34364676	LOC647946 (676 kb)	0.6 (0.5, 0.7)	6.0E-06	0.13	0.22	0.19
2	rs12466517	118546861	INSIG2 (16 kb)	1.4 (1.2, 1.7)	6.1E-06	0.45	0.37	0.38
5	rs6453104	74324825	GCNT4 (34 kb)	0.7 (0.6, 0.8)	6.7E-06	0.33	0.40	0.39
11	rs688858	87652911	CTSC (13 kb)	1.4 (1.2, 1.7)	7.4E-06	0.40	0.33	0.33
2	rs2161829	118573384	INSIG2	1.4 (1.2, 1.7)	9.2E-06	0.49	0.43	0.42
13	rs6561194	44374808	NUFIP1 (37 kb)	1.5 (1.2, 1.8)	1.3E-05	0.28	0.22	0.23
20	rs6080539	16977494	PCSK2 (177 kb)	0.7 (0.6, 0.8)	1.3E-05	0.30	0.40	0.36
20	rs7272442	15223538	MACROD2	1.4 (1.2, 1.7)	1.4E-05	0.46	0.44	0.48
2	rs6542427	118518151	CCDC93 (30 kb)	1.4 (1.2, 1.7)	1.4E-05	0.33	0.26	0.27
4	rs1425419	124785414	LOC285419 (8 kb)	1.6 (1.3, 1.9)	1.5E-05	0.19	0.11	0.15