Table 2.

Comparison of genotype frequencies between breast cancer patients and controls (Set 1)

SNP name	Genetic model	OR(95%CI)	Genotype	Controls(n = 683)	Patients(n = 493)	p-value*	AIC
rs1049982	Recessive	0.93 (0.63-1.37)	T/T	79 (12.8%)	54 (13.4%)	0.72	1309.4
			C/C-C/T	537(87.2%)	350 (86.6%)
rs475043	Recessive	1.27 (0.88-1.85)	G/G	75 (11.5%)	62 (13.3%)	0.21	1454.3
			A/A-A/G	577 (88.5%)	404 (86.7%)
rs511895	Recessive	1.25 (0.86-1.81)	A/A	74 (11.4%)	60(12.9%)	0.25	1451.9
			G/G-A/G	576(88.6%)	404 (87.1%)
rs7104301	Recessive	0.78 (0.51-1.19)	G/G	69 (10.6%)	40 (8.6%)	0.24	1454.3
			A/A-A/G	584 (89.4%)	425 (91.4%)
rs769214	Recessive	0.86 (0.59-1.26)	G/G	80 (12.5%)	57 (12.4%)	0.45	1436
			A/A-A/G	560 (87.5%)	404 (87.6%)
rs5964125	Dominant	1.07 (0.81-1.40)	A/G-G/G	182 (27.8%)	130 (27.8%)	0.65	1462.2
			A/A	472 (72.2%)	337 (72.2%)
rs5964151	Dominan	1.10 (0.83-1.44)	G/T-G/G	181 (27.7%)	133 (28.5%)	0.51	1459.3
			T/T	472 (72.3%)	333 (71.5%)
rs1014852	Recessive	1.22 (0.29-5.19)	T/T	4 (0.6%)	4 (0.9%)	0.79	1462.3
			A/A-A/T	650 (99.4%)	463 (99.1%)
rs11415624	Recessive	0.90 (0.60-1.34)	A/A	73 (11.2%)	47 (10.1%)	0.59	1458.5
			D/D-D/A	579 (88.8%)	419 (89.9%)
rs3736729	Recessive	0.74 (0.54-1.01)	C/C	147 (22.4%)	79 (16.9%)	0.058**	1458.7
			A/A-A/C	508 (77.6%)	387 (83.1%)
rs4140528	Dominant	0.98 (0.77-1.25)	C/T-T/T	297 (45.6%)	206 (44.4%)	0.87	1455.4
			C/C	354 (54.4%)	258 (55.6%)
rs7515191	Recessive	1.21 (0.86-1.70)	A/A	93 (14.2%)	77 (16.5%)	0.22	1461.7
			G/G-A/G	562 (85.8%)	390 (83.5%)
rs7549683	Recessive	1.21 (0.86-1.70)	T/T	93 (14.3%)	76 (16.3%)	0.27	1454.8
			G/G-G/T	556 (85.7%)	391 (83.7%)
rs4812042	Dominant	0.96 (0.75-1.23)	A/G-G/G	357 (55.6%)	258 (55.4%)	0.73	1449.3
			A/A	285 (44.4%)	208 (44.6%)
rs7121	Recessive	0.97 (0.71-1.32)	C/C	130 (20.3%)	93 (19.9%)	0.84	1442.5
			T/T-C/T	509 (79.7%)	374 (80.1%)
rs919196	Dominant	1.12 (0.87-1.45)	C/T-C/C	224 (34.3%)	169 (36.2%)	0.37	1460.2
			T/T	429 (65.7%)	298 (63.8%)
rs406113	Dominant	1.26 (0.98-1.62)	A/C-C/C	314 (51%)	272 (57.6%)	0.066**	1408.9
			A/A	302 (49%)	200 (42.4%)
rs974334	Recessive	2.01 (1.07 -3.80)	G/G	18 (2.8%)	25 (5.4%)	0.03**	1452.9
			C/C-C/G	633 (97.2%)	441 (94.6%)
rs1002149	Dominant	0.95 (0.72-1.26)	G/T-T/T	173 (28.2%)	127 (27.4%)	0.73	1417.4
			G/G	441 (71.8%)	337 (72.6%)
rs2551715	Recessive	0.88 (0.62-1.26)	A/A	94 (14.4%)	60 (12.9%)	0.5	1455.5
			G/G-A/G	557 (85.6%)	405 (87.1%)
rs2911678	Recessive	0.96 (0.48-1.95)	T/T	20 (3.1%)	14 (3%)	0.92	1443.5
			A/A-A/T	629 (96.9%)	445 (97%)
rs8190996	Recessive	1.22 (0.89-1.66)	T/T	126 (19.4%)	96 (20.6%)	0.21	1456.6
			C/C-C/T	524 (80.6%)	371 (79.4%)
rs13041792	Dominant	1.13 (0.88-1.45)	A/G-A/A	240 (36.9%)	181 (39.1%)	0.35	1450.9
			G/G	411 (63.1%)	282 (60.9%)
rs2273684	Recessive	1.21 (0.88-1.65)	G/G	115 (17.6%)	92 (19.8%)	0.24	1456
			T/T-G/T	539 (82.4%)	373 (80.2%)
rs1805754	Dominant	1.31 (1.02- 1.68)	A/C-C/C	257 (40%)	215 (46.1%)	0.034**	1444.2
			A/A	386 (60%)	251 (53.9%)
rs933462	Dominant	1.06 (0.82-1.38)	G/T-G/G	431 (66.6%)	317 (68%)	0.64	1452.2
			T/T	216 (33.4%)	149 (32%)
rs11013291	Recessive	1.09 (0.79-1.51)	C/C	106 (16.3%)	82 (17.6%)	0.6	1458.5
			T/T-C/T	546 (83.7%)	385 (82.4%)
rs2274064	Recessive	0.88 (0.65-1.20)	C/C	136 (21.7%)	91 (20%)	0.42	1413.4
			T/T-C/T	491 (78.3%)	364 (80%)
rs2274065	Dominant	1.21 (0.85-1.72)	A/C-C/C	84 (12.9%)	69 (14.8%)	0.3	1458.9
			A/A	568 (87.1%)	398 (85.2%)
rs2296164	Recessive	0.84 (0.62-1.14)	T/T	143 (22.6%)	91 (19.7%)	0.25	1434.1
			C/C-C/T	491 (77.4%)	370 (80.3%)
rs2072712	Dominant	1.16 (0.84-1.59)	C/T-T/T	108 (16.5%)	88 (18.9%)	0.37	1461.4
			C/C	547 (83.5%)	378 (81.1%)
rs570234	Dominant	1.03 (0.79-1.34)	A/C-C/C	388 (63.2%)	273 (63%)	0.81	1355.7
			A/A	226 (36.8%)	160 (37%)
rs576881	Dominant	1.13 (0.88-1.46)	A/G-G/G	390 (60.6%)	293 (62.9%)	0.33	1448.1
			A/A	254 (39.4%)	173 (37.1%)
rs816296	Dominant	1.20(0.93-1.55)	A/C-A/A	211 (32.5%)	172 (36.8%)	0.17	1455.6
			C/C	438 (67.5%)	295 (63.2%)
rs2779248	Recessive	0.88 (0.60-1.29)	C/C	75 (11.7%)	55 (11.8%)	0.52	1444.5
			T/T-C/T	569 (88.3%)	410 (88.2%)
rs3729508	Dominant	0.90 (0.69-1.18)	A/G-A/A	443 (70.4%)	316 (69%)	0.46	1421.5
			G/G	186 (29.6%)	142 (31%)
rs4827881	Dominant	1.00 (0.78-1.29)	A/C-A/A	246 (37.6%)	177 (37.9%)	0.98	1462.8
			C/C	408 (62.4%)	290 (62.1%)
rs5921682	Dominant	1.12 (0.85-1.47)	A/G-G/G	459 (70.4%)	339 (72.6%)	0.42	1459.8
			A/A	193 (29.6%)	128 (27.4%)
rs490934	Recessive	3.34 (0.57-19.43)	C/C	2 (0.3%)	4 (0.9%)	0.16	1459.6
			G/G-C/G	651 (99.7%)	463(99.1%)
rs1052133	Recessive	1.76 (1.00-3.10)	G/G	34 (5.1%)	28 (8.1%)	0.051**	1124
			C/C-C/G	631 (94.9%)	319 (91.9%)
rs2842980	Recessive	1.40 (0.82-2.37)	T/T	31 (4.9%)	31 (6.7%)	0.22	1439.2
			A/A-A/T	606 (95.1%)	435 (93.3%)
rs2855116	Dominant	0.89 (0.68-1.16)	G/T-G/G	440 (69.3%)	313 (67%)	0.39	1444.1
			T/T	195 (30.7%)	154 (33%)
rs8031	Dominant	0.85 (0.65-1.10)	A/T-A/A	458 (70.6%)	313 (67.2%)	0.22	1454.3
			T/T	191 (29.4%)	153 (32.8%)
rs2284659	Recessive	1.30 (0.92-1.84)	T/T	83 (12.9%)	80 (17.2%)	0.14**	1445.6
			G/G-G/T	560 (87.1%)	386 (82.8%)
rs2301241	Dominant	0.80 (0.60-1.07)	C/T-C/C	460 (74.4%)	348 (71.2%)	0.14**	1350.5
			T/T	158 (25.6%)	141 (28.8%)
rs4135168	Dominant	1.17 (0.90-1.52)	A/G-G/G	238 (39.9%)	183 (43.4%)	0.23	1328
			A/A	359 (60.1%)	239 (56.6%)
rs4135179	Dominant	1.27 (0.97-1.66)	A/G-G/G	178 (28%)	151 (32.8%)	0.085**	1431
			A/A	458 (72%)	310 (67.2%)
rs4135225	Recessive	0.66 (0.45- 0.96)	C/C	104 (16.2%)	48 (10.5%)	0.029**	1431.1
			T/T-C/T	536 (83.8%)	410 (89.5%)
rs2281082	Recessive	1.52 (0.73-3.17)	T/T	15 (2.3%)	16 (3.5%)	0.26	1443.5
			G/G-G/T	627 (97.7%)	447 (96.5%)
rs5756208	Recessive	1.54 (0.77-3.11)	T/T	17 (2.7%)	17 (3.7%)	0.23	1438.5
			A/A-A/T	618 (97.3%)	445 (96.3%)
rs10861201	Recessive	0.69 (0.41-1.17)	A/A	49 (7.6%)	23 (5.1%)	0.16	1411.8
			C/C-A/C	592 (92.4%)	425 (94.9%)
rs4077561	Recessive	1.20 (0.86-1.68)	T/T	92 (14.6%)	80 (17.4%)	0.28	1425
			C/T-T/T	540 (85.4%)	380 (82.6%)
rs4964287	Dominant	1.09 (0.85-1.40)	C/T-T/T	356 (54.4%)	266 (57%)	0.48	1461.9
			C/C	298 (45.6%)	201 (43%)
rs4964778	Dominant	1.17 (0.90-1.51)	C/G-G/G	216 (33.1%)	171 (36.7%)	0.24	1457.3
			C/C	436 (66.9%)	295 (63.3%)
rs4964779	Dominant	1.16 (0.80-1.68)	C/T-C/C	76 (11.8%)	62 (13.3%)	0.43	1451.5
			T/T	569 (88.2%)	405 (86.7%)
rs5018287	Recessive	1.12 (0.82-1.53)	A/A	118 (18%)	91 (19.6%)	0.47	1453.9
			G/G-A/G	536 (82%)	372 (80.4%)
rs737866	Dominant	1.16 (0.90-1.49)	A/G-G/G	298 (49%)	234 (53.4%)	0.25	1364.1
			A/A	310 (51%)	204 (46.6%)
rs10175754	Dominant	0.92 (0.69-1.22)	C/T-C/C	177 (27.8%)	118 (26%)	0.55	1418.6
			T/T	460 (72.2%)	335 (74%)
rs10187719	Recessive	0.80 (0.51-1.26)	T/T	59 (9.9%)	34 (7.9%)	0.34	1353.8
			C/C-C/T	539 (90.1%)	398 (92.1%)
rs1346644	Recessive	1.48 (0.71-3.09)	G/G	16 (2.5%)	15 (3.2%)	0.29	1458
			C/C-C/G	637 (97.5%)	450 (96.8%)
rs1429374	Dominant	1.15 (0.89-1.47)	A/G-A/A	356 (54.9%)	274 (59%)	0.28	1450.4
			G/G	292 (45.1%)	190 (41%)
rs1884725	Recessive	0.71 (0.42-1.22)	A/A	42 (6.5%)	23 (5%)	0.21	1444.1
			G/G-A/G	604 (93.5%)	439 (95%)
rs206801	Recessive	3.42 (0.33-35.82)	T/T	1 (0.2%)	3 (0.6%)	0.27	1462
			C/C-C/T	654 (99.8%)	464 (99.4%)
rs206812	Recessive	0.96 (0.72-1.28)	A/A	159 (24.4%)	111 (23.8%)	0.78	1461.8
			G/G-A/G	494 (75.6%)	356 (76.2%)
rs2073316	Recessive	1.14 (0.84-1.56)	A/A	118 (18.6%)	95 (20.8%)	0.4	1423.7
			G/G-A/G	517 (81.4%)	361 (79.2%)
rs207454	Recessive	4.98 (1.28- 19.34)	C/C	3 (0.5%)	9 (1.9%)	0.012**	1450.3
			A/A-A/C	646 (99.5%)	457 (98.1%)
rs761926	Dominant	0.85 (0.66-1.08)	C/G-G/G	334 (51.1%)	214 (45.8%)	0.18	1459.4
			C/C	319 (48.9%)	253 (54.2%)

CI, confidence interval; OR, odds ratio. *p-values adjusted by age. In bold p-values <0.05. **polymorphisms with a p-value<=0.15. Set 1 (n=1176; cases=493 and controls=683). The best model have been chosen with the criteria of lower AIC (Akaike information criterion) and lower BIC (Bayesian information criterion) values. Only AIC is shown in table.