S2 Table Pleiotropic SqCC risk variants fixed-effects (F-E) meta-analyses.,,,,,,,,,,,,,,,,,,,,,,,,
,,,,,,F-E SqCC meta-analyses,,,,Lung SqCC,,,,Oral/oropharynx SqCC,,,,Larynx SqCC,,,,Esophageal SqCC,,
rsID,Chr:Pos,Chr,Region,EA/OAa,EAFb,OR,SE,P,,OR,SE,P,,OR,SE,P,,OR,SE,P,,OR,SE,P
rs1229984,4:100239319,4,4q23,T/C,0.05,0.80,0.04,1.89E-09,,0.92,0.05,7.35E-02,,0.58,0.08,8.32E-13,,0.67,0.16,1.42E-02,,0.28,0.32,9.28E-05
rs137966363,6:29375802,6,6p22,C/T,0.08,1.20,0.03,2.20E-12,,1.23,0.03,1.25E-10,,1.21,0.05,4.37E-04,,1.01,0.13,9.28E-01,,1.04,0.18,8.05E-01
rs115620922,6:29376385,6,6p22,G/C,0.08,1.20,0.03,2.21E-12,,1.23,0.03,1.25E-10,,1.21,0.05,4.39E-04,,1.01,0.13,9.30E-01,,1.04,0.18,8.07E-01
rs115870917,6:29607101,6,6p22,C/T,0.08,1.24,0.03,2.57E-15,,1.28,0.03,9.83E-14,,1.21,0.06,4.93E-04,,1.09,0.13,5.40E-01,,1.01,0.18,9.49E-01
rs115408932,6:29927722,6,6p22,G/C,0.47,1.10,0.02,1.99E-10,,1.10,0.02,3.89E-07,,1.13,0.03,3.36E-05,,1.03,0.07,7.04E-01,,1.08,0.09,3.60E-01
rs114465838,6:29937977,6,6p22,G/A,0.40,1.12,0.02,5.63E-13,,1.13,0.02,3.62E-10,,1.11,0.03,2.58E-04,,1.09,0.07,1.79E-01,,1.05,0.09,5.83E-01
rs116480994,6:30032522,6,6p22,C/A,0.08,1.23,0.03,4.05E-15,,1.27,0.03,2.10E-13,,1.21,0.06,4.31E-04,,1.08,0.13,5.42E-01,,1.02,0.17,9.05E-01
rs115631432,6:30045199,6,6p22,A/G,0.36,1.11,0.02,4.65E-12,,1.12,0.02,8.02E-09,,1.12,0.03,2.16E-04,,1.10,0.07,1.65E-01,,1.09,0.09,3.40E-01
rs114618975,6:30112795,6,6p22,A/G,0.08,1.22,0.03,1.28E-14,,1.24,0.03,5.19E-12,,1.23,0.05,1.76E-04,,1.15,0.13,2.72E-01,,1.04,0.17,8.24E-01
rs116090375,6:30127805,6,6p22,G/A,0.09,1.22,0.03,2.33E-14,,1.24,0.03,5.05E-12,,1.22,0.05,3.16E-04,,1.14,0.13,2.87E-01,,1.04,0.17,8.31E-01
rs116441981,6:30137209,6,6p22,A/G,0.12,1.18,0.02,5.98E-13,,1.19,0.03,7.02E-10,,1.18,0.05,4.62E-04,,1.15,0.11,2.01E-01,,1.22,0.14,1.53E-01
rs116534499,6:30138162,6,6p22,G/C,0.45,1.09,0.02,5.14E-09,,1.08,0.02,4.57E-05,,1.15,0.03,1.50E-06,,1.04,0.07,5.22E-01,,1.01,0.09,8.97E-01
rs114265059,6:30147230,6,6p22,G/T,0.12,1.18,0.02,7.90E-13,,1.19,0.03,9.66E-10,,1.18,0.05,4.32E-04,,1.15,0.11,2.02E-01,,1.21,0.14,1.63E-01
rs115387234,6:30152467,6,6p22,T/G,0.08,1.23,0.03,6.37E-15,,1.25,0.03,2.02E-12,,1.22,0.06,3.38E-04,,1.17,0.13,2.04E-01,,1.07,0.17,7.06E-01
rs145088312,6:30162505,6,6p22,A/G,0.12,1.18,0.02,4.74E-13,,1.19,0.03,5.61E-10,,1.18,0.05,4.09E-04,,1.14,0.11,2.08E-01,,1.21,0.14,1.69E-01
rs115382475,6:30165662,6,6p22,A/G,0.12,1.18,0.02,5.28E-13,,1.19,0.03,6.28E-10,,1.18,0.05,4.06E-04,,1.14,0.11,2.09E-01,,1.21,0.14,1.70E-01
rs114124113,6:30169092,6,6p22,G/A,0.12,1.18,0.02,4.04E-13,,1.19,0.03,6.28E-10,,1.18,0.05,2.46E-04,,1.14,0.11,2.33E-01,,1.19,0.14,1.99E-01
rs115962467,6:30171284,6,6p22,T/C,0.12,1.18,0.02,5.11E-13,,1.19,0.03,7.11E-10,,1.18,0.05,2.77E-04,,1.14,0.11,2.33E-01,,1.19,0.14,2.01E-01
rs115756918,6:30173538,6,6p22,A/G,0.08,1.23,0.03,5.91E-15,,1.25,0.03,2.03E-12,,1.22,0.06,3.50E-04,,1.18,0.13,1.98E-01,,1.08,0.17,6.52E-01
rs114524376,6:30174428,6,6p22,T/A,0.12,1.18,0.02,4.95E-13,,1.19,0.03,7.09E-10,,1.18,0.05,2.63E-04,,1.13,0.11,2.36E-01,,1.19,0.14,2.03E-01
rs150922079,6:30177939,6,6p22,A/G,0.12,1.18,0.02,5.77E-13,,1.19,0.03,7.79E-10,,1.18,0.05,2.86E-04,,1.14,0.11,2.34E-01,,1.19,0.14,2.01E-01
rs116118489,6:30181883,6,6p22,A/G,0.12,1.18,0.02,4.52E-13,,1.19,0.03,6.40E-10,,1.18,0.05,2.60E-04,,1.13,0.11,2.39E-01,,1.19,0.14,2.05E-01
rs142696802,6:30190040,6,6p22,T/C,0.29,1.12,0.02,2.14E-11,,1.12,0.02,7.44E-08,,1.14,0.03,3.31E-05,,1.05,0.07,4.89E-01,,1.10,0.09,2.96E-01
rs149750519,6:30195038,6,6p22,T/G,0.12,1.18,0.02,8.25E-13,,1.19,0.03,8.55E-10,,1.18,0.05,3.53E-04,,1.13,0.11,2.44E-01,,1.19,0.14,2.10E-01
rs115647250,6:30204399,6,6p22,G/C,0.12,1.17,0.02,1.08E-12,,1.19,0.03,8.46E-10,,1.18,0.05,4.23E-04,,1.13,0.11,2.69E-01,,1.19,0.14,2.16E-01
rs115630448,6:30223428,6,6p22,T/C,0.17,1.14,0.02,2.68E-11,,1.13,0.03,5.25E-07,,1.17,0.04,5.25E-05,,1.11,0.09,2.57E-01,,1.30,0.12,2.51E-02
rs115785414,6:30279130,6,6p22,A/G,0.08,1.23,0.03,1.46E-15,,1.26,0.03,3.99E-13,,1.21,0.05,4.71E-04,,1.17,0.13,2.03E-01,,1.12,0.17,5.07E-01
rs115899777,6:31299899,6,6p21.33,C/T,0.17,1.13,0.02,2.96E-09,,1.11,0.02,3.39E-05,,1.16,0.04,4.56E-05,,1.09,0.13,5.25E-01,,1.55,0.16,6.79E-03
rs115063210,6:31351887,6,6p21.33,A/C,0.35,1.09,0.02,1.12E-08,,1.09,0.02,8.09E-06,,1.13,0.03,6.31E-05,,1.04,0.07,5.75E-01,,1.01,0.09,9.49E-01
rs1800628,6:31546850,6,6p21.33,A/G,0.09,1.25,0.03,2.35E-18,,1.28,0.03,1.54E-15,,1.22,0.05,2.63E-04,,1.18,0.12,1.73E-01,,1.20,0.16,2.35E-01
rs115484360,6:31940897,6,6p21.33,G/A,0.09,1.26,0.03,2.42E-19,,1.29,0.03,1.41E-16,,1.21,0.05,4.41E-04,,1.21,0.12,1.19E-01,,1.24,0.16,1.65E-01
rs116300399,6:32096001,6,6p21.33,A/C,0.09,1.25,0.03,3.41E-18,,1.28,0.03,2.63E-15,,1.21,0.05,4.09E-04,,1.21,0.12,1.07E-01,,1.22,0.16,2.06E-01
rs115860703,6:32131972,6,6p21.32,C/G,0.09,1.25,0.03,3.80E-18,,1.27,0.03,6.94E-15,,1.22,0.05,2.90E-04,,1.25,0.12,6.23E-02,,1.21,0.16,2.26E-01
rs139865833,6:32218120,6,6p21.32,A/G,0.08,1.25,0.03,3.54E-18,,1.27,0.03,1.05E-14,,1.23,0.05,1.66E-04,,1.25,0.12,6.20E-02,,1.20,0.16,2.55E-01
rs115894431,6:32219898,6,6p21.32,A/G,0.09,1.25,0.03,6.78E-18,,1.27,0.03,1.00E-14,,1.21,0.05,3.64E-04,,1.26,0.12,5.20E-02,,1.20,0.16,2.56E-01
rs149131618,6:32226481,6,6p21.32,G/A,0.08,1.25,0.03,1.79E-18,,1.28,0.03,7.02E-15,,1.23,0.05,1.54E-04,,1.27,0.12,4.54E-02,,1.20,0.16,2.55E-01
rs115157812,6:32230256,6,6p21.32,G/T,0.08,1.25,0.03,1.68E-18,,1.28,0.03,6.22E-15,,1.23,0.05,1.48E-04,,1.26,0.12,5.20E-02,,1.20,0.16,2.53E-01
rs150470445,6:32240072,6,6p21.32,A/T,0.08,1.25,0.03,1.82E-18,,1.28,0.03,5.16E-15,,1.23,0.05,1.55E-04,,1.25,0.12,6.56E-02,,1.20,0.16,2.57E-01
rs147151648,6:32252132,6,6p21.32,G/A,0.08,1.25,0.03,1.51E-18,,1.28,0.03,3.37E-15,,1.23,0.05,1.57E-04,,1.25,0.12,6.62E-02,,1.17,0.16,3.16E-01
rs116757844,6:32257199,6,6p21.32,C/T,0.08,1.25,0.03,4.00E-18,,1.28,0.03,9.59E-15,,1.23,0.05,1.60E-04,,1.25,0.12,6.63E-02,,1.17,0.16,3.15E-01
rs114384056,6:32261252,6,6p21.32,G/T,0.09,1.25,0.03,3.88E-18,,1.27,0.03,8.26E-15,,1.23,0.05,1.78E-04,,1.25,0.12,6.64E-02,,1.17,0.16,3.16E-01
rs142144345,6:32263663,6,6p21.32,T/C,0.09,1.25,0.03,3.21E-18,,1.28,0.03,7.28E-15,,1.23,0.05,1.65E-04,,1.25,0.12,6.64E-02,,1.17,0.16,3.16E-01
rs116325871,6:32269457,6,6p21.32,T/C,0.09,1.25,0.03,3.49E-18,,1.27,0.03,7.80E-15,,1.23,0.05,1.69E-04,,1.25,0.12,6.64E-02,,1.17,0.16,3.15E-01
rs116245742,6:32274882,6,6p21.32,A/C,0.09,1.25,0.03,4.15E-18,,1.27,0.03,9.23E-15,,1.23,0.05,1.73E-04,,1.25,0.12,6.66E-02,,1.18,0.16,3.10E-01
rs150977343,6:32275621,6,6p21.32,T/C,0.09,1.25,0.03,5.78E-18,,1.27,0.03,1.35E-14,,1.23,0.05,1.75E-04,,1.25,0.12,6.66E-02,,1.18,0.16,3.04E-01
rs147338561,6:32280591,6,6p21.32,C/T,0.08,1.27,0.03,1.34E-17,,1.30,0.03,3.34E-14,,1.24,0.06,1.41E-04,,1.27,0.13,6.81E-02,,1.20,0.17,2.96E-01
rs114999843,6:32284108,6,6p21.32,G/T,0.08,1.26,0.03,6.45E-18,,1.28,0.03,2.35E-14,,1.25,0.06,9.92E-05,,1.24,0.12,8.06E-02,,1.18,0.16,3.13E-01
rs116667074,6:32285362,6,6p21.32,T/C,0.09,1.25,0.03,3.63E-18,,1.28,0.03,8.66E-15,,1.23,0.05,1.86E-04,,1.24,0.12,6.68E-02,,1.19,0.16,2.62E-01
rs114288718,6:32288952,6,6p21.32,A/G,0.09,1.25,0.03,4.37E-18,,1.27,0.03,1.04E-14,,1.22,0.05,1.89E-04,,1.24,0.12,6.68E-02,,1.19,0.16,2.59E-01
rs116636123,6:32290208,6,6p21.32,T/C,0.09,1.25,0.03,4.40E-18,,1.27,0.03,1.05E-14,,1.22,0.05,1.90E-04,,1.24,0.12,6.68E-02,,1.20,0.16,2.59E-01
rs139165151,6:32295652,6,6p21.32,C/T,0.09,1.25,0.03,3.94E-18,,1.28,0.03,8.97E-15,,1.22,0.05,1.95E-04,,1.24,0.12,6.69E-02,,1.20,0.16,2.58E-01
rs116669008,6:32303692,6,6p21.32,A/T,0.09,1.25,0.03,5.83E-18,,1.27,0.03,1.28E-14,,1.22,0.05,2.10E-04,,1.24,0.12,6.71E-02,,1.20,0.16,2.57E-01
rs115007147,6:32305544,6,6p21.32,G/A,0.09,1.25,0.03,4.53E-18,,1.27,0.03,1.06E-14,,1.22,0.05,2.06E-04,,1.25,0.12,6.17E-02,,1.20,0.16,2.57E-01
rs114138262,6:32315511,6,6p21.32,G/T,0.09,1.25,0.03,4.62E-18,,1.27,0.03,1.09E-14,,1.22,0.05,2.08E-04,,1.25,0.12,6.18E-02,,1.20,0.16,2.56E-01
rs114142816,6:32325562,6,6p21.32,A/G,0.09,1.25,0.03,7.04E-18,,1.27,0.03,1.57E-14,,1.22,0.05,2.10E-04,,1.24,0.12,6.79E-02,,1.20,0.16,2.58E-01
rs145864686,6:32340070,6,6p21.32,T/C,0.34,1.10,0.02,1.68E-09,,1.10,0.02,5.18E-06,,1.13,0.03,1.35E-04,,1.14,0.07,6.77E-02,,1.04,0.09,7.05E-01
rs114937304,6:32340871,6,6p21.32,T/C,0.09,1.25,0.03,2.62E-18,,1.28,0.03,6.11E-15,,1.23,0.05,1.64E-04,,1.24,0.12,7.46E-02,,1.20,0.16,2.61E-01
rs116676210,6:32358201,6,6p21.32,C/G,0.09,1.25,0.03,4.83E-18,,1.27,0.03,1.05E-14,,1.23,0.05,1.61E-04,,1.23,0.12,8.48E-02,,1.18,0.16,2.84E-01
rs147461705,6:32368462,6,6p21.32,A/G,0.09,1.25,0.03,6.45E-18,,1.27,0.03,1.36E-14,,1.23,0.05,1.56E-04,,1.22,0.12,1.03E-01,,1.20,0.16,2.58E-01
rs115613607,6:32381280,6,6p21.32,C/G,0.09,1.25,0.03,6.99E-18,,1.27,0.03,1.20E-14,,1.23,0.05,1.71E-04,,1.22,0.12,9.47E-02,,1.17,0.16,3.13E-01
rs115100928,6:32387432,6,6p21.32,A/G,0.09,1.25,0.03,4.84E-18,,1.27,0.03,1.16E-14,,1.23,0.05,1.21E-04,,1.22,0.12,9.57E-02,,1.17,0.16,3.20E-01
rs114125569,6:32395726,6,6p21.32,G/A,0.09,1.25,0.03,6.54E-18,,1.27,0.03,1.63E-14,,1.23,0.05,1.15E-04,,1.22,0.12,1.01E-01,,1.18,0.16,3.11E-01
rs114390392,6:32398841,6,6p21.32,G/A,0.09,1.25,0.03,6.74E-18,,1.27,0.03,1.64E-14,,1.23,0.05,1.23E-04,,1.22,0.12,9.70E-02,,1.18,0.16,3.07E-01
rs114351019,6:32399337,6,6p21.32,C/T,0.09,1.25,0.03,6.08E-18,,1.27,0.03,1.64E-14,,1.23,0.05,1.12E-04,,1.22,0.12,9.69E-02,,1.18,0.16,3.05E-01
rs114573742,6:32408497,6,6p21.32,G/A,0.09,1.25,0.03,4.79E-18,,1.27,0.03,1.79E-14,,1.23,0.05,8.36E-05,,1.22,0.12,9.64E-02,,1.19,0.16,2.87E-01
rs116815995,6:32414435,6,6p21.32,T/C,0.09,1.25,0.03,8.77E-18,,1.27,0.03,1.81E-14,,1.23,0.05,1.55E-04,,1.22,0.12,9.83E-02,,1.19,0.16,2.81E-01
rs114575468,6:32583328,6,6p21.32,C/T,0.37,1.14,0.02,5.40E-14,,1.14,0.02,1.99E-09,,1.14,0.03,4.64E-05,,1.27,0.08,4.31E-03,,1.05,0.11,6.76E-01
rs9271377,6:32587165,6,6p21.32,G/T,0.38,1.13,0.02,8.87E-13,,1.13,0.02,2.06E-08,,1.13,0.03,8.62E-05,,1.26,0.08,4.74E-03,,1.06,0.11,5.93E-01
rs113067973,6:32591609,6,6p21.32,G/A,0.41,1.16,0.02,4.82E-19,,1.17,0.02,3.01E-14,,1.15,0.03,1.23E-05,,1.27,0.08,5.14E-03,,1.02,0.11,8.36E-01
rs9273326,6:32623219,6,6p21.32,T/C,0.46,0.91,0.02,1.24E-08,,0.93,0.02,2.21E-04,,0.85,0.03,3.39E-07,,0.98,0.10,8.51E-01,,0.98,0.13,8.82E-01
rs9273329,6:32623242,6,6p21.32,G/A,0.52,0.91,0.02,1.14E-08,,0.93,0.02,2.13E-04,,0.85,0.03,3.29E-07,,0.98,0.10,8.33E-01,,0.98,0.13,8.80E-01
rs9273330,6:32623300,6,6p21.32,C/T,0.58,0.91,0.02,1.37E-08,,0.93,0.02,3.30E-04,,0.85,0.03,2.91E-07,,0.97,0.11,7.76E-01,,0.98,0.15,8.94E-01
rs113663338,6:32624847,6,6p21.32,G/T,0.58,0.91,0.02,1.96E-07,,0.93,0.02,3.35E-04,,0.87,0.03,2.97E-05,,0.96,0.11,7.50E-01,,0.91,0.15,5.35E-01
rs9273415,6:32627310,6,6p21.32,C/T,0.61,0.89,0.02,1.23E-11,,0.91,0.02,4.51E-06,,0.83,0.03,1.64E-08,,0.94,0.13,6.34E-01,,0.87,0.17,4.08E-01
rs1063355,6:32627714,6,6p21.32,T/G,0.47,0.91,0.02,4.10E-10,,0.92,0.02,3.44E-06,,0.85,0.03,3.00E-07,,1.00,0.07,9.41E-01,,0.98,0.09,8.04E-01
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rs1063349,6:32627906,6,6p21.32,T/C,0.51,0.91,0.02,2.88E-10,,0.91,0.02,5.25E-06,,0.85,0.03,2.88E-07,,0.99,0.07,8.78E-01,,0.95,0.10,6.34E-01
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rs149751104,6:32671800,6,6p21.32,G/T,0.11,1.22,0.02,2.43E-16,,1.27,0.03,4.53E-15,,1.19,0.05,2.84E-04,,1.07,0.11,5.25E-01,,1.01,0.14,9.67E-01
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rs115926869,6:32673893,6,6p21.32,A/C,0.11,1.22,0.02,2.16E-16,,1.27,0.03,3.19E-15,,1.19,0.05,3.17E-04,,1.07,0.11,5.37E-01,,1.00,0.14,9.78E-01
rs114867306,6:32679326,6,6p21.32,T/C,0.11,1.22,0.02,5.04E-16,,1.27,0.03,4.69E-15,,1.18,0.05,4.81E-04,,1.06,0.11,5.63E-01,,1.00,0.14,9.98E-01
rs7857345,9:22087473,9,9p21.3,T/C,0.30,1.11,0.02,5.55E-10,,1.09,0.02,1.34E-05,,1.14,0.03,3.73E-05,,1.18,0.07,1.91E-02,,1.07,0.10,4.63E-01
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aEA=Effect allele/OA=other allele; bEAF=average effect allele frequency,,,,,,,,,,,,,,,,,,,,,,,,