Table 2.

Description of SCN genes variants among epilepsy cases and healthy controls.

Gene	SNP ID	SNP positiona	Variant Consequence	Cases (n = 296)			Controls (n = 293)
				MA	MAF	HWE p value	MAF	HWE p value
SCN1A	rs3812718	2:166053034	Intron	T	0.46	0.73	0.40	0.05
	rs2298771	2:166036278	Missense	C	0.46	0.41	0.49	0.91
	rs10167228	2:166042592	Intron	T	0.46	0.41	0.49	0.91
	rs146733308	2:165991324	Missense	T	0.00	N/A	0.00	N/A
	rs35735053	2:165991411	Missense	G	0.00	N/A	0.00	N/A
	rs3749029	2:165991504	Missense	T	0.00	N/A	0.00	N/A
	rs6432858	2:166033433	Intron	C	0.46	0.41	0.49	1.00
	rs10194956	2:166046065	Intron	G	0.46	0.72	0.40	0.06
	rs146878122	2:166009822	Missense	A	0.00	0.10	0.00	N/A
	rs121918817	2:166045080	Missense	T	0.00	N/A	0.00	N/A
	rs121918624	2:166052882	Stop Gained	A	0.00	0.10	0.00	0.10
	rs2169312	2:166071386	Intron	C	0.17	0.68	0.18	0.69
	rs1461197	2:166067962	Intron	A	0.33	0.11	0.36	0.08
	rs13405797	2:166062652	Intron	A	0.17	0.84	0.17	0.53
	rs4667866	2:166059523	Intron	G	0.05	0.59	0.06	0.61
	rs10188577	2:166059387	Intron	C	0.28	0.001	0.23	0.87
	rs1020853	2:166023272	Intron	T	0.22	1.00	0.22	0.86
	rs7587026	2:166122240	Intron	A	0.24	0.01	0.19	1.0
	rs1381105	2:166068661	Intron	G	0.24	0.43	0.25	0.54
	rs2162600	2:166069891	Intron	C	0.18	0.55	0.18	0.69
	rs10182473	2:166017213	Intron	C	0.22	1.00	0.22	0.87
	rs16851381	2:166056929	Intron	G	0.05	1.00	0.06	0.61
	rs4667869	2:166066849	Intron	G	0.18	0.55	0.17	0.55
	rs11692675	2:166069918	Intron	C	0.29	1e-3	0.24	0.53
	rs10497275	2:165990220	Intron	G	0.05	0.59	0.06	0.61
	rs7577411	2:165989284	Non Coding Transcript	A	0.02	1.00	0.03	1e-3
	rs10930195	2:166045896	Intron	A	0.46	0.72	0.40	0.04
	rs6432861	2:166046718	Intron	T	0.45	0.051	0.40	0.14
	rs7580482	2:166046935	Synonymous	T	0.48	0.73	0.51	0.48
	rs13383628	2:166047150	Intron	T	0.46	0.64	0.4	0.051
	rs1841546	2:166052594	Intron	T	0.43	0.53	0.4	0.03
	rs6722462	2:166075016	Intron	C	0.33	0.09	0.36	0.10
	rs6432860	2:166041354	Synonymous	A	0.46	0.35	0.49	1.00
	rs994399	2:166048970	Intron	G	0.48	0.73	0.51	0.41
	rs1542484	2:166048865	Intron	A	0.46	0.72	0.4	0.05
	rs1461193	2:166047836	Intron	G	0.46	0.41	0.49	0.91
	rs11690959	2:166047515	Intron	A	0.45	0.73	0.40	0.07
	rs7601520	2:166036571	Intron	G	0.45	0.40	0.49	0.81
SCN2A	rs12467383	2:165369259	Intron	A	0.06	1.00	0.07	1.00
	rs2304016	2:165311993	Intron	G	0.00	N/A	0.00	N/A
	rs17183814	2:165295879	Missense	A	0.04	1e-3	0.04	5e-4
	rs1965757	2:165308377	Intron	G	0.29	0.16	0.32	0.68
	rs353139	2:165289717	Intron	C	0.36	0.30	0.38	0.90
	rs7581811	2:165300655	Intron	C	0.36	0.8	0.39	0.90
	rs2116658	2:165310162	Intron	T	0.38	0.08	0.41	0.33
	rs12993173	2:165326704	Intron	G	0.37	0.45	0.40	1.00
	rs4667485	2:165363235	Intron	C	0.28	0.89	0.20	0.58
	rs1469649	2:165370597	Intron	G	0.29	0.78	0.21	1.00
	rs3816002	2:165342576	Intron	G	0.00	N/A	0.00	N/A
	rs1579865	2:165335204	Intron	A	0.37	0.17	0.42	0.54
	rs935403	2:165328783	Intron	C	0.34	0.24	0.38	0.80
	rs7592445	2:165303176	Intron	C	0.29	0.26	0.31	0.78
	rs2119067	2:165270773	Intron	C	0.18	1.00	0.16	0.66
	rs2119068	2:165270664	Intron	C	0.42	0.90	0.43	1.00
	rs10197716	2:165268464	Intron	G	0.27	0.30	0.27	0.12
	rs353112	2:165280573	Intron	C	0.45	0.10	0.44	0.40
	rs6740895	2:165283510	Intron	C	0.23	0.11	0.26	0.37
	rs3943809	2:165344371	Intron	G	0.06	1.00	0.07	1.00
	rs16850331	2:165292743	Intron	T	0.07	0.63	0.08	1.00
	rs12614399	2:165293790	Intron	C	0.07	0.63	0.08	1.00
	rs10182570	2:165253124	Intron	C	0.26	0.45	0.27	0.18
	rs1446579	2:165267091	Intron	G	0.46	0.41	0.47	0.56
SCN3A	rs7598098	2:165109768	Intron	C	0.22	0.49	0.26	0.36
	rs11903851	2:165134943	Intron	T	0.26	<1e-4	0.25	1.00
	rs1439807	2:165143358	Intron	G	0.28	<1e-4	0.26	0.88
	rs12615864	2:165175282	Intron	A	0.07	0.14	0.09	0.72
	rs16850186	2:165167410	Intron	A	0.10	0.33	0.14	0.22
	rs1439806	2:165135256	Intron	A	0.26	0.35	0.23	0.17
	rs7596422	2:165151706	Intron	G	0.50	0.56	0.48	0.82
SCN1B	rs3746255	19:35033642	Synonymous	T	0.00	N/A	0.00	N/A
	rs745394799	19:35034182	Intron	T	0.00	N/A	0.00	N/A
	rs2305748	19:35039234	Missense	T	0.00	N/A	0.00	N/A
	rs72550243	19:35039332	Intron	T	0.00	1.00	0.00	1.00
	rs55742440	19:35033920	Missense	T	0.45	0.03	0.43	0.72
	rs67701503	19:35034035	Missense	A	0.19	0.01	0.16	1.00
	rs67486287	19:35034040	Missense	C	0.18	0.02	0.15	1.00
SCN2B	rs8192613	11:118167098	Intron	T	0.38	0.81	0.40	0.27
	rs8192614	11:118166849	3 Prime UTR	A	0.13	1.00	0.13	0.11
SCN3B	rs3851100	11:123653202	Intron	C	0.07	0.18	0.07	0.64
	rs1783901	11:123642798	Intron	T	0.28	0.19	0.24	0.33
SCN8A	rs303777	12:51754412	Intron	A	0.27	0.1	0.25	0.76
	rs11169883	12:51597548	Intron	T	0.41	0.06	0.46	0.24
	rs303778	12:51750944	Intron	G	0.15	1.00	0.13	1.00

^aChromosome positions are based on NCBI Human Genome Assembly Build.

MA: minor allele; MAF: minor allele frequency; HWE: Hardy—Weinberg equilibrium.