Supplementary Table 7

(1)

Europe North America

Region rs Gene OR P OR

4q23 rs14678804:9994113 METAP1 G A Geno 0.48 1.73E-05 0.70 4q23 rs1162034 4:1000681LOC10050C T Geno 0.53 9.24E-05 0.73 9q34.12 rs928674 9:1339520LAMC3 G A 0.89 1.20 6.07E-03 1.26 9q34.12 rs19971789:1339538LAMC3 C A Geno 1.21 3.87E-03 1.24 9q34.12 rs73658919:1339539LAMC3 G A 0.94 1.18 1.28E-02 1.29 9q34.12 rs77452479:1339625LAMC3 G T 0.88 1.20 2.71E-03 1.23 6p21.32 rs62404576:3237601LOC10192A C Geno 0.68 8.01E-06 0.80 6p21.32 rs14900556:3252736HLA-DRB6A C Geno 0.66 5.46E-08 0.84 6p21.32 rs53470576:32562023 G A 0.77 0.31 1.35E-05 0.18 6p21.32 rs1124813 6:32567551 G A 0.99 0.67 2.00E-06 0.79 6p21.32 rs62405656:32567784 C A 0.99 0.67 2.00E-06 0.79 6p21.32 rs9270911 6:32572202 C T 1.00 0.30 3.83E-06 0.14 6p21.32 rs13995766:32574983 A G 0.66 0.53 7.62E-06 0.66 6p21.32 rs1126483 6:32583900 G A 0.90 0.61 1.22E-06 0.73 6p21.32 rs12819336:32586507 T C 1.00 0.62 3.17E-07 0.77 6p21.32 rs1140141 6:32588842 G A 0.79 0.59 7.26E-06 0.71 6p21.32 rs35224566:32592313 G A Geno 0.66 3.35E-08 0.85 6p21.32 rs92716876:32592985 A G 0.85 0.27 1.89E-03 0.28 6p21.32 rs34720986:32593270 C G 1.00 0.66 3.59E-08 0.84 6p21.32 rs34518866:32594103 A G 0.99 0.66 3.62E-08 0.85 6p21.32 rs1147861 6:32596878 G A 0.86 0.63 2.66E-07 0.82 6p21.32 rs92723466:3260437HLA-DQA1G A 1.00 0.25 9.97E-05 0.15 6p21.32 rs10479896:3260525HLA-DQA1C A 1.00 0.30 3.60E-06 0.14 6p21.32 rs1130034 6:3260527HLA-DQA1T C 1.00 0.25 9.94E-05 0.15 6p21.32 rs92724416:3260538HLA-DQA1T G 0.97 0.30 5.01E-06 0.15 6p21.32 rs77513766:3260543HLA-DQA1C G 1.00 0.25 1.03E-04 0.15 6p21.32 rs92725536:3260700HLA-DQA1G T 0.96 0.28 1.74E-05 0.15 6p21.32 rs92725836:3260745HLA-DQA1C T 0.89 0.25 1.52E-05 0.17 6p21.32 rs92726016:3260765HLA-DQA1T A 0.70 1.28 2.11E-05 1.17 6p21.32 rs92726076:3260773HLA-DQA1G A 0.91 0.29 7.84E-06 0.15 6p21.32 rs92726136:3260782HLA-DQA1A G 1.00 0.25 8.64E-05 0.15 6p21.32 rs92726256:3260801HLA-DQA1T C 0.99 0.27 3.66E-05 0.15 6p21.32 rs92726296:3260809HLA-DQA1G T 1.00 0.25 9.98E-05 0.15 6p21.32 rs1129740 6:3260910HLA-DQA1G A 1.00 0.25 9.92E-05 0.15 6p21.32 rs10716306:3260912HLA-DQA1T C 1.00 0.25 9.85E-05 0.15 6p21.32 rs92727226:3260940HLA-DQA1C T 0.95 0.29 1.48E-05 0.14 6p21.32 rs92727236:3260942HLA-DQA1T C 1.00 0.25 9.73E-05 0.15 6p21.32 rs34843906:3261005HLA-DQA1T G 1.00 0.25 9.89E-05 0.15 6p21.32 rs10650366:3261102 HLA-DQA1A G Geno 0.80 1.28E-04 0.87 6p21.32 rs92730216:3261172 HLA-DQA1A G Geno 0.79 4.97E-05 0.87 6p21.32 rs92730346:3261187 HLA-DQA1C A Geno 0.80 1.15E-04 0.87 6p21.32 rs92730786:3261230HLA-DQA1A T 0.75 1.28 6.43E-05 1.16 Supplementary Table 7 Overall oral and pharynx cancer results (5x10-7< P >5x10-8 )

Chr:posa

Effect

(2)

6p21.32 rs92730826:3261233HLA-DQA1C T 0.87 0.32 3.52E-06 0.15 6p21.32 rs92730836:3261234HLA-DQA1T C 0.86 0.26 9.83E-05 0.16 6p21.32 rs92730846:3261239HLA-DQA1T C 0.95 0.26 9.63E-05 0.15 6p21.32 rs6240411 6:3261241HLA-DQA1A G Geno 0.63 7.94E-07 0.74 6p21.32 rs69268946:3261243HLA-DQA1A G 0.95 0.77 2.31E-06 0.88 6p21.32 rs92730886:3261248HLA-DQA1A C 0.93 0.26 6.90E-05 0.16 6p21.32 rs92731096:3261262HLA-DQA1G A 0.81 1.24 3.02E-05 1.18 6p21.32 rs92731676:3261316HLA-DQA1C A 0.91 0.27 4.84E-05 0.16 6p21.32 rs92732156:3261371HLA-DQA1G A 0.91 0.28 4.20E-05 0.16 6p21.32 rs92732166:3261374HLA-DQA1C A 0.90 0.28 3.62E-05 0.16 6p21.32 6:32613826:3261382HLA-DQA1C T 0.94 0.26 8.82E-05 0.16 6p21.32 rs92732426:3261408HLA-DQA1T C 0.96 0.26 9.99E-05 0.15 6p21.32 rs92732686:3261433HLA-DQA1C T 0.75 1.37 9.94E-06 1.16 6p21.32 rs17612516:3261488HLA-DQA1G A Geno 0.80 1.50E-04 0.87 6p21.32 rs17612546:3261531HLA-DQA1G A 0.97 0.24 1.57E-04 0.16 6p21.32 rs17843576:3261540HLA-DQA1C T 1.00 0.25 1.01E-04 0.15 6p21.32 rs17843576:3261542HLA-DQA1C T 0.98 0.26 5.71E-05 0.15 6p21.32 rs17612576:3261545HLA-DQA1G A Geno 0.80 1.40E-04 0.87 6p21.32 rs17843586:3261555HLA-DQA1A G 0.99 0.25 8.43E-05 0.15 6p21.32 rs17612596:3261557HLA-DQA1G A 0.94 0.28 2.61E-05 0.15 6p21.32 rs17843586:3261565HLA-DQA1A C 0.99 0.25 8.87E-05 0.15 6p21.32 rs17612626:3261570HLA-DQA1A C Geno 0.80 1.17E-04 0.87 6p21.32 rs17612636:3261571HLA-DQA1G C 1.00 0.25 1.00E-04 0.15 6p21.32 rs17843606:3262024HLA-DQA1G A Geno 0.79 4.01E-05 0.87 6p21.32 rs17843606:3262028HLA-DQA1G A Geno 0.76 2.09E-06 0.88 6p21.32 6:32620286:32620286 T C 0.98 0.30 3.09E-06 0.14 6p21.32 rs17612786:3262031HLA-DQA1A G Geno 0.79 6.33E-05 0.87 6p21.32 rs17612786:3262034HLA-DQA1G A Geno 0.80 7.11E-05 0.87 6p21.32 rs17612806:3262035HLA-DQA1G A Geno 0.80 9.27E-05 0.87 6p21.32 rs17843606:3262039HLA-DQA1C A Geno 0.80 7.62E-05 0.87 6p21.32 rs17612816:3262046HLA-DQA1G T 0.84 1.24 4.23E-05 1.19 6p21.32 rs17612856:3262062HLA-DQA1A T 0.99 0.25 1.06E-04 0.15 6p21.32 rs17843616:3262066HLA-DQA1T G 0.93 0.29 1.93E-05 0.15 6p21.32 rs17612926:3262097HLA-DQA1A G 0.98 0.24 1.43E-04 0.15 6p21.32 6:3262113 6:32621132 C T 0.67 1.31 8.91E-06 1.20 6p21.32 rs92733266:32623219 A G Geno 0.80 1.10E-04 0.87 6p21.32 rs92733296:32623242 G A 1.00 0.25 1.10E-04 0.15 6p21.32 rs92733306:32623300 C T 0.99 0.25 1.00E-04 0.15 6p21.32 rs92733386:32623393 A T 0.91 0.25 9.13E-05 0.16 6p21.32 rs92733396:32623430 G A Geno 0.79 4.86E-05 0.87 6p21.32 6:32623586:32623585 A G 0.78 1.27 1.92E-04 1.25 6p21.32 rs53315576:32624038 T C 0.70 1.28 3.09E-05 1.19 6p21.32 rs1123915 6:32624660 T C 0.92 0.30 8.21E-06 0.15 6p21.32 rs72852266:32624715 A C Geno 0.79 6.32E-05 0.87 6p21.32 rs74824386:32624731 A G 0.97 0.26 6.96E-05 0.15 6p21.32 rs19967736:32624828 I D Geno 0.80 7.20E-05 0.87 6p21.32 rs69052826:32626015 A C 1.00 1.22 2.32E-05 1.18 6p21.32 rs28584176:32626119 A G Geno 0.66 3.52E-08 0.84

(3)

6p21.32 rs12055446:3262673HLA-DQB1A G 1.00 0.22 1.79E-05 0.18 6p21.32 rs92734006:3262712HLA-DQB1C T 0.91 0.28 1.20E-05 0.15 6p21.32 rs92734366:3262751HLA-DQB1G T 0.85 1.28 1.21E-05 1.17 6p21.32 rs10633556:3262771HLA-DQB1T G 1.00 0.25 1.00E-04 0.15 6p21.32 rs10633496:3262790HLA-DQB1T C 1.00 0.25 8.90E-05 0.15 6p21.32 rs10633486:3262792HLA-DQB1A G 1.00 0.25 1.10E-04 0.15 6p21.32 rs92734806:3262810HLA-DQB1A G Geno 1.27 1.52E-05 1.18 6p21.32 rs92734936:3262824HLA-DQB1T C 1.00 0.25 1.00E-04 0.15 6p21.32 rs92734976:3262829HLA-DQB1T C 0.99 0.24 2.30E-04 0.15 6p21.32 rs92735246:3262859HLA-DQB1T C 1.00 0.25 1.08E-04 0.15 6p21.32 rs1140343 6:3262913HLA-DQB1T G 0.99 0.25 9.92E-05 0.15 6p21.32 rs92741776:3263040HLA-DQB1A G Geno 0.81 2.04E-04 0.86 6p21.32 rs36222416:3263434HLA-DQB1G A Geno 1.24 4.25E-06 1.17 6p21.32 rs92745696:3263509HLA-DQB1A C Geno 1.25 2.20E-06 1.17 6p21.32 rs38287896:3263575HLA-DQB1C A Geno 0.80 1.20E-04 0.87 6p21.32 rs38287906:3263580HLA-DQB1T C 1.00 0.25 9.98E-05 0.15 6p21.32 rs92746606:3263643HLA-DQB1A G 1.00 0.25 9.96E-05 0.15

a_{SNP position according to NCBI genome build 37 (Hg19)}

b_{Geno=genotyped, SNP, INFO, Rsq is the average across imputation batches.} c_{Frequency of the effect allele.}

(4)

North America South America

P OR P OR P

3.55E-02 0.44 1.45E-03 0.02 0.03 0.55 5.61E-08 0.171 3.42E-02 0.44 1.12E-03 0.02 0.03 0.59 2.51E-07 0.149 3.62E-04 1.29 1.42E-02 0.14 0.12 1.24 3.79E-07 0.792 7.03E-04 1.27 1.55E-02 0.12 0.10 1.24 4.29E-07 0.922 1.25E-04 1.28 1.88E-02 0.12 0.10 1.24 4.39E-07 0.633 5.11E-04 1.25 1.88E-02 0.16 0.14 1.22 2.77E-07 0.915 7.05E-03 0.84 9.28E-02 0.07 0.09 0.76 2.22E-07 0.204 1.96E-02 0.90 2.80E-01 0.09 0.11 0.78 1.14E-07 0.018 8.16E-04 0.07 3.33E-01 0.39 0.42 0.19 2.38E-07 0.112 4.41E-03 0.94 5.82E-01 0.06 0.08 0.77 4.50E-07 0.063 4.40E-03 0.94 5.81E-01 0.06 0.08 0.77 4.46E-07 0.063 1.81E-03 0.06 3.41E-01 0.42 0.45 0.16 3.50E-07 0.049 6.26E-03 0.78 2.16E-01 0.03 0.04 0.62 2.92E-07 0.255 3.28E-03 0.88 3.61E-01 0.04 0.06 0.71 9.01E-08 0.108 3.93E-03 0.90 3.99E-01 0.05 0.07 0.73 6.86E-08 0.048 4.39E-03 0.83 2.68E-01 0.04 0.05 0.68 2.66E-07 0.225 1.92E-02 0.89 2.27E-01 0.09 0.11 0.78 5.50E-08 0.019 2.31E-05 0.07 4.92E-01 0.15 0.17 0.23 4.95E-07 0.251 1.73E-02 0.89 2.27E-01 0.09 0.11 0.78 5.01E-08 0.021 1.96E-02 0.89 2.19E-01 0.09 0.11 0.78 5.39E-08 0.021 1.77E-02 0.88 2.59E-01 0.07 0.09 0.76 2.50E-07 0.034 9.49E-04 0.10 1.22E-01 0.38 0.41 0.17 3.15E-07 0.316 1.48E-03 0.09 1.69E-01 0.43 0.46 0.17 9.42E-08 0.083 9.50E-04 0.10 1.27E-01 0.38 0.41 0.17 3.31E-07 0.31 1.16E-03 0.08 2.05E-01 0.41 0.44 0.17 1.19E-07 0.084 8.85E-04 0.10 1.22E-01 0.38 0.42 0.17 3.01E-07 0.32 9.54E-04 0.10 1.61E-01 0.40 0.43 0.17 1.49E-07 0.155 3.60E-04 0.05 4.35E-01 0.46 0.49 0.17 1.29E-07 0.125 1.03E-03 1.13 1.06E-01 0.43 0.40 1.20 5.63E-08 0.37 1.58E-03 0.09 2.06E-01 0.45 0.48 0.17 1.95E-07 0.107 9.35E-04 0.10 1.28E-01 0.38 0.42 0.17 3.00E-07 0.297 1.00E-03 0.10 1.48E-01 0.39 0.42 0.17 2.22E-07 0.209 9.50E-04 0.10 1.27E-01 0.38 0.41 0.17 3.32E-07 0.311 9.34E-04 0.10 1.27E-01 0.38 0.41 0.17 3.24E-07 0.311 9.32E-04 0.10 1.27E-01 0.38 0.41 0.17 3.21E-07 0.31 1.66E-03 0.10 1.38E-01 0.41 0.44 0.17 1.96E-07 0.151 9.23E-04 0.10 1.27E-01 0.38 0.41 0.17 3.16E-07 0.31 9.52E-04 0.10 1.29E-01 0.38 0.41 0.17 3.38E-07 0.307 8.48E-04 0.91 1.49E-01 0.38 0.41 0.86 4.34E-07 0.309 1.07E-03 0.91 1.21E-01 0.38 0.42 0.86 2.19E-07 0.256 1.05E-03 0.90 1.15E-01 0.38 0.41 0.86 3.57E-07 0.333 1.88E-03 1.14 7.22E-02 0.50 0.46 1.19 2.15E-07 0.373

Meta-analysisd Frq.c cases Frq.c control s Phet

(5)

1.54E-03 0.12 1.06E-01 0.44 0.47 0.19 5.24E-08 0.104 5.98E-04 0.10 1.44E-01 0.42 0.46 0.18 2.23E-07 0.322 8.46E-04 0.11 1.20E-01 0.39 0.42 0.17 2.70E-07 0.315 1.67E-03 0.91 4.48E-01 0.05 0.07 0.73 5.34E-08 0.073 1.67E-03 0.92 1.90E-01 0.42 0.46 0.85 9.95E-08 0.063 6.74E-04 0.10 1.32E-01 0.40 0.43 0.17 1.88E-07 0.285 4.46E-04 1.04 5.74E-01 0.47 0.44 1.17 3.73E-07 0.121 7.06E-04 0.11 1.08E-01 0.41 0.44 0.18 1.21E-07 0.278 7.41E-04 0.12 8.01E-02 0.41 0.44 0.18 8.27E-08 0.289 5.41E-04 0.12 1.01E-01 0.41 0.45 0.18 6.94E-08 0.267 5.63E-04 0.11 9.73E-02 0.39 0.43 0.18 1.30E-07 0.341 9.67E-04 0.11 1.21E-01 0.39 0.42 0.17 3.26E-07 0.31 2.46E-03 1.13 9.54E-02 0.50 0.48 1.20 2.40E-07 0.091 1.00E-03 0.90 9.64E-02 0.38 0.41 0.86 3.36E-07 0.384 6.14E-04 0.10 1.28E-01 0.39 0.42 0.17 2.84E-07 0.372 9.62E-04 0.10 1.26E-01 0.38 0.41 0.17 3.36E-07 0.312 1.01E-03 0.10 1.39E-01 0.39 0.42 0.17 2.76E-07 0.249 9.69E-04 0.91 1.27E-01 0.38 0.41 0.86 4.30E-07 0.34 9.79E-04 0.10 1.30E-01 0.38 0.42 0.17 3.17E-07 0.291 1.37E-03 0.11 1.15E-01 0.40 0.43 0.17 1.77E-07 0.208 8.09E-04 0.10 1.21E-01 0.38 0.42 0.17 2.44E-07 0.311 1.05E-03 0.90 1.09E-01 0.38 0.42 0.86 3.39E-07 0.343 9.74E-04 0.10 1.26E-01 0.38 0.41 0.17 3.40E-07 0.311 7.16E-04 0.90 1.11E-01 0.39 0.42 0.85 1.07E-07 0.272 2.16E-03 0.92 1.67E-01 0.43 0.47 0.85 1.01E-07 0.064 1.58E-03 0.09 1.91E-01 0.43 0.46 0.17 1.08E-07 0.073 7.59E-04 0.92 1.85E-01 0.38 0.42 0.86 3.19E-07 0.227 1.01E-03 0.91 1.25E-01 0.38 0.41 0.86 2.82E-07 0.275 8.45E-04 0.91 1.35E-01 0.38 0.41 0.86 3.04E-07 0.296 1.05E-03 0.91 1.26E-01 0.38 0.41 0.86 3.13E-07 0.279 1.02E-04 1.04 5.39E-01 0.49 0.46 1.18 1.03E-07 0.141 1.01E-03 0.10 1.24E-01 0.38 0.41 0.17 3.57E-07 0.317 1.48E-03 0.09 1.71E-01 0.41 0.45 0.17 2.81E-07 0.146 1.10E-03 0.11 1.21E-01 0.39 0.42 0.16 4.57E-07 0.353 4.78E-04 1.09 2.73E-01 0.42 0.39 1.21 5.11E-08 0.178 9.50E-04 0.91 1.20E-01 0.38 0.41 0.86 3.34E-07 0.326 9.50E-04 0.10 1.27E-01 0.38 0.41 0.16 3.53E-07 0.32 8.23E-04 0.11 1.18E-01 0.38 0.42 0.17 2.59E-07 0.327 5.30E-04 0.10 1.39E-01 0.41 0.45 0.18 1.71E-07 0.339 7.24E-04 0.91 1.34E-01 0.38 0.42 0.85 1.67E-07 0.246 7.21E-05 1.04 6.25E-01 0.23 0.20 1.21 3.14E-07 0.154 6.54E-04 1.05 5.35E-01 0.34 0.32 1.19 4.32E-07 0.148 1.02E-03 0.11 1.24E-01 0.43 0.46 0.18 6.49E-08 0.147 7.91E-04 0.91 1.26E-01 0.38 0.41 0.86 2.03E-07 0.272 1.08E-03 0.12 7.23E-02 0.39 0.43 0.17 1.49E-07 0.343 9.30E-04 0.91 1.20E-01 0.38 0.41 0.86 2.48E-07 0.286 6.42E-05 1.01 8.50E-01 0.48 0.45 1.16 1.14E-07 0.055 1.27E-02 0.92 3.76E-01 0.09 0.11 0.78 7.25E-08 0.015

(6)

8.65E-05 0.02 7.02E-01 0.45 0.47 0.15 4.47E-07 0.014 1.29E-03 0.11 1.09E-01 0.46 0.50 0.18 7.53E-08 0.205 4.53E-04 1.07 3.51E-01 0.53 0.50 1.18 1.12E-07 0.125 9.62E-04 0.10 1.24E-01 0.38 0.41 0.17 3.27E-07 0.314 9.59E-04 0.10 1.27E-01 0.38 0.41 0.17 3.11E-07 0.3 9.20E-04 0.10 1.24E-01 0.38 0.42 0.17 3.33E-07 0.323 8.86E-04 1.06 4.20E-01 0.23 0.19 1.19 2.27E-07 0.166 9.38E-04 0.10 1.24E-01 0.38 0.41 0.17 3.19E-07 0.314 1.17E-03 0.12 7.29E-02 0.38 0.41 0.17 3.86E-07 0.459 8.80E-04 0.10 1.28E-01 0.38 0.41 0.17 3.30E-07 0.317 1.02E-03 0.10 1.22E-01 0.38 0.42 0.17 3.36E-07 0.317 4.54E-04 0.90 9.63E-02 0.38 0.41 0.85 1.86E-07 0.434 2.09E-04 1.01 9.12E-01 0.45 0.42 1.16 1.25E-07 0.032 1.95E-04 1.01 8.54E-01 0.44 0.41 1.16 5.64E-08 0.031 8.77E-04 0.91 1.35E-01 0.38 0.41 0.86 3.74E-07 0.318 9.46E-04 0.10 1.27E-01 0.38 0.41 0.17 3.30E-07 0.311 9.50E-04 0.10 1.27E-01 0.38 0.41 0.17 3.31E-07 0.311