Table 3. Variants identified in NFKB1 by direct sequencing in 94 TRS cases and controls.

SNP	Region	Allele	Genotype			Effect	Risk Allele	RAF		F difference
				case (%)	control (%)			case	control
rs28362491	P	ATTG/-	ins/ins∶ins/-∶-/-	24.4 ∶ 46.7 ∶ 28.9	31.7 ∶ 47.8 ∶ 20.5		del	0.522	0.444	0.078
rs11940017	P	T>C	TT∶TC∶CC	85.9 ∶ 14.1 ∶ 0	95.7 ∶ 4.3 ∶ 0		C	0.071	0.022	0.049
rs11944443	p	A>G	AA∶AG∶GG	85.9 ∶ 14.1 ∶ 0	95.7 ∶ 4.3 ∶ 0		G	0.071	0.022	0.049
rs41477752	I2	T>-	TT∶T/-∶-/-	87.0 ∶ 13.0 ∶ 0	95.6 ∶ 4.4 ∶ 0		del	0.065	0.022	0.043
IVS2-60 A>G	I2	A>G	AA∶AG∶GG	98.9 ∶ 1.1 ∶ 0	100.0 ∶ 0 ∶ 0		G	0.005	0	0.005
c.692 G>T	E8	G>T	GG∶GT∶TT	98.9 ∶ 1.1 ∶ 0	100.0 ∶ 0 ∶ 0	R231L	T	0.005	0	0.005
rs4648049	I12	C>T	CC∶CT∶TT	86.2 ∶ 13.8 ∶ 0	95.5 ∶ 4.5 ∶ 0		T	0.069	0.022	0.047
rs4648050	I12	T>C	TT∶TC∶CC	25.5 ∶ 36.2 ∶ 38.3	27.0 ∶ 49.4 ∶ 23.6		C	0.564	0.483	0.081
IVS12+21 C>T	I12	C>T	CC∶CT∶TT	98.9 ∶ 1.1 ∶ 0	100.0 ∶ 0 ∶ 0		T	0.005	0	0.005
rs1020760	I11	G>C	GG∶GC∶CC	42.1 ∶ 40.0 ∶ 17.9	24.7 ∶ 50.6 ∶ 24.7		G	0.621	0.5	0.121
IVS11-56 T>C	I11	T>C	TT∶TC∶CC	97.9 ∶ 2.1 ∶ 0	98.9 ∶ 1.1 ∶ 0		C	0.011	0.006	0.005
c.1116 G>A	E12	G>A	GG∶GA∶AA	98.9 ∶ 1.1 ∶ 0	100.0 ∶ 0 ∶ 0	S372S	A	0.005	0	0.005
IVS13+196 T>G	I13	T>G	TT∶TG∶GG	98.9 ∶ 1.1 ∶ 0	100.0 ∶ 0 ∶ 0		G	0.005	0	0.005
c.1601 G>A	E15	G>A	GG∶GA∶AA	98.9 ∶ 1.1 ∶ 0	100.0 ∶ 0 ∶ 0	R534H	A	0.005	0	0.005
IVS15+12 C>G	I15	C>G	CC∶CG∶GG	98.9 ∶ 1.1 ∶ 0	100.0 ∶ 0 ∶ 0		G	0.005	0	0.005
IVS15+40 G>A	I15	G>A	GG∶GA∶AA	98.9 ∶ 1.1 ∶ 0	100.0 ∶ 0 ∶ 0		A	0.005	0	0.005
rs4648095	I17	T>C	TT∶TC∶CC	81.1 ∶ 18.9 ∶ 0	93.6 ∶ 9.6 ∶ 0		C	0.095	0.032	0.063
rs4648110	I22	T>A	TT∶TA∶AA	92.6 ∶ 7.4 ∶ 0	87.1 ∶ 12.9 ∶ 0		T	0.963	0.935	0.028
rs4648117	I22	C>T	CC∶CT∶TT	80.6 ∶ 19.4 ∶ 0	94.3 ∶ 5.7 ∶ 0		T	0.097	0.028	0.069
IVS22-23 C>T	I22	C>T	CC∶CT∶TT	97.8 ∶ 2.2 ∶ 0	100.0 ∶ 0 ∶ 0		T	0.011	0	0.011
rs3817685	I22	G>C	GG∶GC∶CC	32.6 ∶ 41.3 ∶ 26.1	20.5 ∶52.3 ∶ 27.3		G	0.533	0.466	0.067
rs35795162	I23	-/A	-/-∶-/A∶AA	77.4 ∶ 20.4 ∶ 2.2	90.9 ∶ 9.1 ∶ 0		A	0.124	0.045	0.079
IVS23-44 G>A	I23	G>A	GG∶GA∶AA	98.9 ∶ 1.1 ∶ 0	100.0 ∶ 0 ∶ 0		A	0.005	0	0.005

Risk allele means the allele with higher frequency in schizophrenia as compared with controls;

RAF: risk allele frequency.

P: promoter, I : intron.