Table 1.

Associations of SPT/Recurrence with the Top 20 Chromosomal SNPs

SNP	Host gene	Pathway	Position in host gene	Chromosome region	Allelic change	Genotype Counts*			Best-fitting model			Number of times in Bootstrap Sample P<0.01
						SPT	No SPT	Model	HR (95% CI)**	P Value	q value
rs12359892	MKI67	Cell cycle	3’ region	10q26	T>C	101/14/27	221/38/18	Recessive	2.65 (1.72–4.11)	1.25×10−5	0.042	96
rs359974	NHEJ1	DNA repair	3’ region	2q35	T>C	93/44/10	213/76/4	Recessive	4.26 (2.18–8.32)	2.15×10−5	0.042	81
rs7781436	CDK6	Cell cycle	Intron 4	7q21–q22	T>C	97/41/9	186/104/3	Recessive	4.51 (2.22–9.17)	3.24×10−5	0.042	68
rs876435	TNFRSF10B	Apoptosis	3’ region	8p22–p21	A>G	51/63/33	114/148/31	Recessive	2.26 (1.52–3.36)	6.04×10−5	0.042	90
rs12888332	MNAT1	DNA repair	Intron 7	14q23	T>G	125/19/3	280/10/3	Dominant	2.57 (1.62–4.09)	6.27×10−5	0.042	88
rs506008	GSTM4	Carcinogen metabolism	sSNP in exon 7 §	1p13	G>A	94/46/3	232/54/1	Dominant	2.09 (1.46–3.00)	6.30×10−5	0.042	91
rs7561607	GLI2	SHH stem cell	Intron 2	2q14	C>T	26/82/39	103/128/62	Dominant	2.30 (1.49–3.55)	1.63×10−4	0.094	94
rs6684195	RNF2	Epigentic regulation	Intron 1	1q25	A>G	50/64/33	111/150/32	Recessive	2.12 (1.43–3.14)	1.93×10−4	0.097	87
rs17387169	PROM1	EMT, stem cell	Intron 13	4p15	G>A	129/19/2	202/85/6	Dominant	0.42 (0.26–0.67)	2.71×10−4	0.121	92
rs7168671	IGF1R	Growth factor signaling	Intron 7	15q26	C>T	94/44/9	194/93/6	Recessive	3.98 (1.87–8.44)	3.22×10−4	0.13	61
rs7591	AXIN1	WNT stem cell	3’ UTR	16p13	A>T	33/93/21	110/124/59	Dominant	2.03 (1.37–3.01)	4.10×10−4	0.15	89
rs2306536	CHFR	Cell cycle	nsSNP §§ in exon 15	12q24	C>T	87/49/11	88/97/8	Recessive	3.14 (1.65–5.99)	5.13×10−4	0.172	70
rs7118388	CAT	Carcinogen metabolism	5’ region	11p13	G>A	51/66/30	70/139/84	Additive	0.67 (0.53–0.84)	5.64×10−4	0.175	85
rs2237724	CFTR	Carcinogen metabolism	Intron 3	7q31-q32	G>A	92/45/10	198/89/6	Recessive	3.12 (1.62–5.98)	6.30×10−4	0.181	68
rs604337	GSTM4	Carcinogen metabolism	5’ region	1p13	C>T	94/50/3	223/64/6	Dominant	1.84 (1.29–2.61)	6.80×10−4	0.183	71
rs3826537	MRC2	Growth factor signaling	sSNP in exon 30	17q23	A>G	67/63/17	88/150/55	Dominant	0.57 (0.41–0.79)	8.41×10−4	0.202	84
rs9562605	BRCA2	DNA repair	Intron 1	13q12–q13	C>T	107/36/4	168/114/11	Dominant	0.54 (0.37–0.78)	9.34×10−4	0.202	80
rs2300181	CAT	Carcinogen metabolism	Intron 6	11p13	G>A	76/58/13	163/124/6	Recessive	2.67 (1.49–4.78)	9.38×10−4	0.202	79
rs11047917	KRAS	RAS signaling	Intron 2	12p12	C>T	123/24/0	271/22/0	Dominant	2.12 (1.36–3.31)	9.51×10−4	0.202	69
rs9622978¶	PDGFB	Growth factor signaling	Intron 5	22q12–q13	G>T	49/63/35	98/160/35	Recessive	1.92 (1.30–2.85)	1.08×10−3	0.213	76

^*Genotype counts: common homozygous/ heterozygous/rare homozygous genotype

^**Adjusted for age, gender, ethnicity, smoking status, tumor site, tumor stage, and treatment.

^§sSNP, synonymous SNP;

^§§nsSNP, nonsynonous SNP.

^¶Shaded SNPs were those with a p<0.01 at least 80% of the times in bootstrapping.