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Table 1 Analysis of genotype data from melanoma cases and controls for polymorphisms on chromosome 9p21 locus

From: Variants at the 9p21 locus and melanoma risk

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    
  1. Values in bold indicate statistical significance.