Background
Methods
Study populations
Selection and genotyping of the polymorphisms
Statistical analysis
Bioinformatic analysis
Results
SNP | Cases (%) | Controls (%) | OR | 95% CI | P value |
---|---|---|---|---|---|
rs751173
| |||||
TT | 211 (27.2) | 358 (31.1) | Reference | ||
TC | 384 (49.6) | 573 (49.7) | 1.18 | 0.94 –1.47 | |
CC |
179 (23.1)
|
221 (19.2)
|
1.43
|
1.09-1.87
|
0.04
|
TC+CC |
563 (72.7)
|
794 (68.9)
|
1.25
|
1.01-1.54
|
0.04
|
T allele | 806 (52.1) | 1286 (56) | Reference | ||
C allele |
742 (47.9)
|
1015 (44.1)
|
1.19
|
1.04–1.37
|
0.01
|
MAF | 0.48 | 0.44 | |||
rs4636294
| |||||
GG | 169 (21.9) | 280 (24.3) | Reference | ||
AG | 375 (48.5) | 605 (52.5) | 1.07 | 0.84–1.36 | |
AA |
229 (29.6)
|
268 (23.2)
|
1.41
|
1.08–1.85
|
0.02
|
AG+AA | 604 (78.1) | 873 (75.7) | 1.17 | 0.93–1.47 | 0.16 |
G allele | 713 (46.1) | 1165 (50.5) | Reference | ||
A allele |
833 (53.9)
|
1141 (49.5)
|
1.19
|
1.04–1.36
|
0.01
|
MAF | 0.54 | 0.50 | |||
rs2218220
| |||||
TT | 167 (21.6) | 281 (24.4) | Reference | ||
CT | 379 (49) | 607 (52.7) | 1.09 | 0.86–1.39 | |
CC
|
228 (29.5)
|
264 (22.9)
|
1.45
|
1.11–1.91
|
0.01
|
TC+CC | 607 (78.4) | 871 (75.6) | 1.20 | 0.96–1.51 | 0.12 |
T allele | 713 (46.1) | 1169 (50.7) | Reference | ||
C allele |
835 (53.9)
|
1135 (49.3)
|
1.21
|
1.05–1.38
|
0.007
|
MAF | 0.54 | 0.49 | |||
rs1335510
| |||||
TT | 323 (41.8) | 406 (35.4) | Reference | ||
TG |
352 (45.6)
|
568 (49.5)
|
0.79
|
0.64–0.97
| |
GG |
97 (12.5)
|
173 (15.1)
|
0.67
|
0.49–0.91
|
0.01
|
TG+GG |
449 (58.2)
|
741 (64.6)
|
0.76
|
0.63–0.93
|
0.007
|
T allele | 998 (64.6) | 1380 (60.2) | Reference | ||
G allele |
546 (35.4)
|
914 (39.8)
|
0.81
|
0.71–0.94
|
0.004
|
MAF | 0.35 | 0.40 | |||
rs1341866
| |||||
TT | 316 (40.8) | 398 (34.6) | Reference | ||
TC |
361 (46.6)
|
576 (50)
|
0.81
|
0.66–0.99
| |
CC |
97 (12.5)
|
177 (15.4)
|
0.66
|
0.49–0.90
|
0.02
|
TC+CC |
458 (59.2)
|
753 (65.4)
|
0.77
|
0.63–0.94
|
0.01
|
T allele | 993 (64.2) | 1372 (59.6) | Reference | ||
C allele |
555 (35.9)
|
930 (40.4)
|
0.82
|
0.71–0.94
|
0.004
|
MAF | 0.36 | 0.40 | |||
rs935053
| |||||
AA | 172 (22.3) | 293 (25.4) | Reference | ||
AG | 373 (48.3) | 601 (52) | 1.10 | 0.87–1.40 | |
GG |
228 (29.5)
|
259 (22.5)
|
1.48
|
1.13–1.94
|
0.009
|
AG+GG | 601 (78 ) | 860 (74.6) | 1.22 | 0.97–1.53 | 0.08 |
A allele | 717 (46.4) | 1187 (51.5) | Reference | ||
G allele |
829 (53.6)
|
1119 (48.5)
|
1.22
|
1.06–1.39
|
0.004
|
MAF | 0.54 | 0.49 | |||
rs10757257
| |||||
GG | 320 (41.3) | 407 (35.4) | Reference | ||
GA |
360 (46.5)
|
567 (49.3)
|
0.83
|
0.68–1.02
| |
AA |
94 (12.1)
|
177 (15.4)
|
0.65
|
0.48–0.88
|
0.02
|
GA+AA |
454 (58.7)
|
744 (64.6)
|
0.79
|
0.65–0.96
|
0.02
|
G allele | 1000 (64.6) | 1381 (60) | Reference | ||
A allele |
548 (35.4)
|
921 (40)
|
0.81
|
0.71–0.94
|
0.004
|
MAF | 0.35 | 0.40 | |||
rs7023329
| |||||
AA | 230 (29.7) | 290 (25.2) | Reference | ||
AG | 377 (48.7) | 576 (50) | 0.84 | 0.67–1.06 | |
GG | 167 (21.6) | 287 (24.9) | 0.74 | 0.56–0.96 | 0.08 |
AG+GG |
544 (70.3)
|
863 (74.9)
|
0.81
|
0.65–1.00
|
0.05
|
A allele | 837 (54.1) | 1156 (50.1) | Reference | ||
G allele |
711 (45.9)
|
1150 (49.9)
|
0.86
|
0.75–0.98
|
0.02
|
MAF | 0.46 | 0.50 | |||
rs10811629
| |||||
AA | 313 (40.4) | 395 (34.4) | Reference | ||
AG |
362 (46.8)
|
579 (50.4)
|
0.83
|
0.68–1.03
| |
GG |
99 (12.8)
|
174 (15.2)
|
0.70
|
0.52–0.95
|
0.05
|
AG+GG |
461 (59.6)
|
753 (65.6)
|
0.80
|
0.66–0.98
|
0.03
|
A allele | 988 (63.8) | 1369 (59.6) | Reference | ||
G allele |
560 (36.2)
|
927 (40.4)
|
0.84
|
0.73–0.97
|
0.02
|
MAF | 0.36 | 0.40 | |||
rs1011970
| |||||
GG | 549 (71.3) | 850 (74.1) | Reference | ||
GT | 190 (24.7) | 277 (24.2) | 1.03 | 0.82–1.29 | |
TT |
31 (4)
|
19 (1.7)
|
2.24
|
1.22–4.13
|
0.04
|
GT+TT | 221 (28.7) | 296 (25.8) | 1.11 | 0.89–1.38 | 0.35 |
G allele | 1288 (83.6) | 1977 (86.3) | Reference | ||
T allele | 252 (16.4) | 315 (13.7) | 1.18 | 0.97- 1.42 | 0.10 |
MAF | 0.17 | 0.14 | |||
CDKN2A
tagging polymorphysms
| |||||
SNP
|
Cases (%)
|
Controls (%)
|
OR
|
95% CI
|
P value
|
rs3731257
| |||||
GG | 398 (52) | 595 (51.8) | Reference | ||
GA | 302 (39.5) | 455 (39.6) | 0.94 | 0.77–1.15 | |
AA | 65 (8.5) | 98 (8.5) | 0.89 | 0.63–1.27 | 0.73 |
GA+AA | 367 (48) | 553 (48.2) | 0.93 | 0.77–1.13 | 0.46 |
G allele | 1098 (71.8) | 1645 (71.7) | Reference | ||
A allele | 432 (28.2) | 651 (28.4) | 0.94 | 0.81–1.09 | 0.43 |
MAF | 0.28 | 0.28 | |||
rs11515
| |||||
GG | 538 (69.7) | 796 (69.6) | Reference | ||
GC | 214 (27.7) | 316 (27.7) | 0.96 | 0.78–1.19 | |
CC | 20 (2.6) | 31 (2.7) | 0.91 | 0.50–1.67 | 0.91 |
GC +CC | 234 (30.3) | 347 (30.4) | 0.96 | 0.78–1.18 | 0.68 |
G allele | 1290 (83.6) | 1908 (83.5) | Reference | ||
C allele | 254 (16.5) | 378 (16.5) | 0.96 | 0.80–1.15 | 0.66 |
MAF | 0.17 | 0.17 | |||
rs3088440
| |||||
CC | 660 (85.4) | 1020 (90) | Reference | ||
CT |
108 (14)
|
108 (9.5)
|
1.52
|
1.13–2.05
| |
TT | 5 (0.7) | 5 (0.4) | 1.50 | 0.40–5.58 |
0.02
|
CT+TT |
113 (14.6)
|
113 (10)
|
1.52
|
1.14–2.04
|
0.005
|
C allele | 1428 (92.4) | 2148 (94.8) | Reference | ||
T allele |
118 (7.6)
|
118 (5.2)
|
1.48
|
1.12–1.96
|
0.005
|
MAF | 0.08 | 0.05 | |||
rs2518719
| |||||
AA | 541 (70.8) | 808 (70.4) | Reference | ||
AG | 206 (27) | 320 (27.9) | 1.04 | 0.84–1.30 | |
GG | 17 (2.2) | 19 (1.7) | 1.58 | 0.79–3.19 | 0.42 |
AG+GG | 223 (29.2) | 339 (29.6) | 1.07 | 0.87–1.33 | 0.51 |
A allele | 1288(84.3) | 1936 (84.4) | Reference | ||
G allele | 240 (15.7) | 358 (15.6) | 1.09 | 0.91–1.31 | 0.36 |
MAF | 0.16 | 0.16 | |||
rs2811708
| |||||
GG | 369 (46.8) | 563 (49.1) | Reference | ||
GT | 332 (43) | 475 (41.5) | 1.09 | 0.89–1.33 | |
TT | 71 (9.2) | 108 (9.4) | 1.05 | 0.74–1.48 | 0.70 |
GT + TT | 403 (52.2) | 583 (50.9) | 1.08 | 0.89–1.31 | 0.42 |
G allele | 1070 (69.3) | 1601 (69.9) | Reference | ||
T allele | 474 (30.7) | 691 (30.2) | 1.05 | 0.91–1.22 | 0.52 |
MAF | 0.31 | 0.30 | |||
rs3731239
| |||||
AA | 356 (46.8) | 494 (43) | Reference | ||
AG | 318 (41.8) | 536 (46.6) | 0.84 | 0.68–1.03 | |
GG | 86 (11.3) | 120 (10.4) | 1.08 | 0.78–1.50 | 0.13 |
AG+GG | 404 (53.2) | 656 (57) | 0.88 | 0.73–1.07 | 0.20 |
A allele | 1030 (67.8) | 1524 (66.3) | Reference | ||
G allele | 490 (32.2) | 776 (33.7) | 0.97 | 0.84–1.12 | 0.65 |
MAF | 0.33 | 0.34 | |||
rs2811710
| |||||
CC | 286 (37) | 450 (39.3) | Reference | ||
CT | 355 (45.9) | 542 (47.3) | 1.03 | 0.82–1.27 | |
TT | 132 (17.1) | 154 (13.4) | 1.40 | 1.05–1.87 | 0.06 |
CT+TT | 487 (63) | 696 (60.7) | 1.10 | 0.91–1.35 | 0.30 |
C allele | 927 (60) | 1442 (62.9) | Reference | ||
T allele |
619 (40)
|
850 (37.1)
|
1.15
|
1.00–1.32
|
0.05
|
MAF | 0.40 | 0.37 | |||
rs3218020
| |||||
GG | 254 (32.8) | 381 (33.2) | Reference | ||
GA | 375 (48.5) | 560 (48.8) | 0.97 | 0.78–1.20 | |
AA | 145 (18.7) | 206 (17.9) | 0.96 | 0.73–1.27 | 0.95 |
GA+AA | 520 (67.2) | 766 (66.8) | 0.97 | 0.79–1.18 | 0.74 |
G allele | 883 (57) | 1322 (57.6) | Reference | ||
A allele | 665 (43) | 972 (42.4) | 0.98 | 0.85–1.12 | 0.76 |
MAF | 0.43 | 0.42 | |||
rs3218009
| |||||
CC | 650 (84) | 965 (83.8) | Reference | ||
CG | 118 (15.3) | 180 (15.6) | 1.01 | 0.77–1.31 | |
GG | 6 (0.8) | 6 (0.5) | 1.96 | 0.61–6.29 | 0.52 |
CG+GG | 124 (16) | 186 (16.2) | 1.04 | 0.80–1.34 | 0.79 |
C allele | 1418 (91.6) | 2110 (91.7) | Reference | ||
G allele | 130 (8.4) | 192 (8.3) | 1.06 | 0.83–1.35 | 0.63 |
MAF | 0.08 | 0.08 | |||
rs3217992
| |||||
CC | 229 (29.9) | 341 (29.7) | Reference | ||
CT | 380 (49.7) | 565 (49.2) | 0.95 | 0.76–1.19 | |
TT | 156 (20.4) | 243 (21.2) | 0.89 | 0.68–1.17 | 0.72 |
CT+TT | 536 (70.1) | 808 (70.3) | 0.94 | 0.76–1.15 | 0.53 |
C allele | 838 (54.8) | 1247 (54.3) | Reference | ||
T allele | 692 (45.2) | 1051 (45.7) | 0.95 | 0.83–1.08 | 0.42 |
MAF | 0.45 | 0.46 | |||
rs1063192
| |||||
AA | 316 (40.9) | 445 (38.8) | Reference | ||
AG | 365 (47.3) | 537 (46.9) | 0.99 | 0.80–1.22 | |
GG | 91 (11.8) | 164 (14.3) | 0.89 | 0.65–1.20 | 0.72 |
AG+GG | 456 (59.1) | 701 (61.2) | 0.97 | 0.79–1.17 | 0.72 |
A allele | 997 (64.6) | 1427 (62.3) | Reference | ||
G allele | 547 (35.4) | 865 (37.7) | 0.95 | 0.83–1.10 | 0.51 |
MAF | 0.35 | 0.38 | |||
rs573687
| |||||
GG | 380 (49.3) | 532 (46.4) | Reference | ||
GA | 329 (42.7) | 501 (43.7) | 0.95 | 0.78–1.17 | |
AA | 62 (8) | 114 (9.9) | 0.86 | 0.61–1.22 | 0.68 |
GA+AA | 391 (50.7) | 615 (53.6) | 0.94 | 0.77–1.14 | 0.50 |
G allele | 1089 (70.6) | 1565 (68.2) | Reference | ||
A allele | 453 (29.4) | 729 (31.8) | 0.94 | 0.81–1.09 | 0.40 |
MAF | 0.29 | 0.32 | |||
rs13298881
| |||||
TT | 565 (73.8) | 862 (75.2) | Reference | ||
TC | 183 (23.9) | 262 (22.8) | 1.14 | 0.91–1.43 | |
CC | 18 (2.4) | 23 (2) | 1.26 | 0.65–2.45 | 0.46 |
TC+CC | 201 (26.2) | 285 (24.9) | 1.15 | 0.92–1.43 | 0.22 |
T allele | 1313 (85.7) | 1986 (86.6) | Reference | ||
C allele | 219 (14.3) | 308 (13.4) | 1.14 | 0.93–1.38 | 0.21 |
MAF | 0.14 | 0.13 | |||
rs545226
| |||||
AA | 207 (26.8) | 300 (26.1) | Reference | ||
AG | 378 (48.9) | 577 (50.3) | 0.88 | 0.70–1.11 | |
GG | 188 (24.3) | 271 (23.6) | 0.93 | 0.71–1.22 | 0.55 |
AG+GG | 566 (73.2) | 848 (73.9) | 0.90 | 0.72–1.11 | 0.32 |
A allele | 792 (51.2) | 1177 (51.3) | Reference | ||
G allele | 754 (48.8) | 1119 (48.7) | 0.96 | 0.84–1.10 | 0.57 |
MAF | 0.49 | 0.49 | |||
rs10811640
| |||||
GG | 184 (24.1) | 298 (26.1) | Reference | ||
GT | 371 (48.5) | 565 (49.4) | 1.02 | 0.81–1.29 | |
TT | 210 (27.5) | 280 (24.5) | 1.12 | 0.86–1.46 | 0.68 |
GT+TT | 581 (76) | 845 (73.9) | 1.05 | 0.84–1.32 | 0.65 |
G allele | 739 (48.3) | 1161 (50.8) | Reference | ||
T allele | 791 (51.7) | 1125 (49.2) | 1.06 | 0.92–1.21 | 0.42 |
MAF | 0.52 | 0.49 |