Table 3.

SNP effects on odds of developing cancer (dominant genetic model)

SCCHN (all 5 anatomic subsites, combined)Oral cavity cancerHypopharyngeal cancerLaryngeal cancer
No. of cases/controlsaAdjusted ORb (95% CI)PcNo. of cases/controlsAdjusted ORb (95% CI)PcNo. of cases/controlsAdjusted ORb (95% CI)PcNo. of cases/controlsAdjusted ORb (95% CI)Pc
GeneSNPMajor/minor allelesHomozygous for major alleleOne or two copies of minor alleleHomozygous for major alleleOne or two copies of minor alleleHomozygous for major alleleOne or two copies of minor alleleHomozygous for major alleleOne or two copies of minor allele
Alcohol metabolism genes
ADH1Brs12507573C/A371/386852/9350.96 (0.87–1.06)1.0057/386115/9350.94 (0.78–1.14)1.0015/38639/9351.03 (0.74–1.42)1.00137/386305/9350.94 (0.82–1.08)1.00
rs1042026A/G712/744511/5781.00 (0.91–1.10)1.0094/74478/5781.06 (0.88–1.26)1.0036/74418/5780.89 (0.65–1.22)1.00264/744178/5780.96 (0.84–1.10)1.00
rs7673353C/T1,124/1,23999/831.01 (0.83–1.23)1.00161/1,23911/830.88 (0.60–1.30)1.0048/1,2396/830.84 (0.51–1.40)1.00402/1,23940/831.04 (0.79–1.36)1.00
rs17028834T/C1,138/1,26585/571.28 (1.03–1.59)1.00159/1,26513/571.50 (1.01–2.25)1.0048/1,2656/571.71 (1.00–2.95)1.00408/1,26534/571.49 (1.11–2.01)0.54
rs1693457T/C803/860419/4611.01 (0.92–1.11)1.00114/86058/4610.99 (0.82–1.19)1.0036/86018/4610.94 (0.69–1.28)1.00294/860148/4611.02 (0.89–1.17)1.00
rs1229984dG/A1,192/1,24331/790.72 (0.57–0.91)0.35169/1,2433/790.63 (0.35–1.15)1.0053/1,2431/790.62 (0.22–1.70)1.00429/1,24313/790.79 (0.57–1.12)1.00
rs1159918G/T402/468821/8541.07 (0.97–1.18)1.0060/468112/8541.03 (0.86–1.24)1.0014/46840/8541.17 (0.83–1.64)1.00154/468288/8541.05 (0.91–1.21)1.00
rs1229982G/T699/775524/5471.00 (0.91–1.10)1.0097/77575/5470.95 (0.80–1.14)1.0035/77519/5470.80 (0.59–1.09)1.00241/775201/5471.05 (0.92–1.19)1.00
ADH1Crs2298753T/C1,002/1,117221/2051.12 (1.00–1.27)1.00140/1,11732/2051.12 (0.89–1.41)1.0046/1,1178/2051.16 (0.78–1.75)1.00366/1,11776/2051.10 (0.93–1.31)1.00
rs1614972C/T539/585684/7371.00 (0.92–1.09)1.0085/58587/7370.93 (0.78–1.10)1.0026/58528/7370.83 (0.61–1.11)1.00192/585250/7370.96 (0.85–1.10)1.00
rs1391088C/A1,045/1,119178/2031.01 (0.89–1.14)1.00142/1,11930/2031.07 (0.85–1.34)1.0050/1,1194/2030.71 (0.41–1.20)1.00381/1,11961/2031.05 (0.88–1.26)1.00
rs1693482eC/T527/585694/7351.05 (0.95–1.15)1.0075/58597/7351.00 (0.83–1.20)1.0024/58530/7351.18 (0.87–1.60)1.00186/585256/7351.09 (0.95–1.25)1.00
rs1631460C/G519/574703/7481.04 (0.95–1.14)1.0074/57497/7480.99 (0.83–1.19)1.0024/57430/7481.17 (0.86–1.58)1.00184/574258/7481.08 (0.94–1.23)1.00
rs11936869C/G611/645612/6760.98 (0.90–1.07)1.0090/64582/6760.96 (0.81–1.14)1.0028/64526/6760.86 (0.64–1.16)1.00221/645221/6760.93 (0.82–1.06)1.00
ADH4rs29001227A/T1,119/1,253104/691.25 (1.02–1.53)1.00157/1,25315/691.31 (0.90–1.91)1.0048/1,2536/691.38 (0.81–2.34)1.00401/1,25341/691.39 (1.05–1.84)1.00
rs1126672C/T720/758503/5641.01 (0.92–1.10)1.0093/75879/5641.08 (0.90–1.28)1.0038/75816/5640.82 (0.60–1.13)1.00257/758185/5641.06 (0.93–1.21)1.00
rs4699710T/C640/684583/6381.01 (0.93–1.11)1.0077/68495/6381.12 (0.94–1.33)1.0034/68420/6380.86 (0.64–1.16)1.00230/684212/6381.05 (0.93–1.20)1.00
rs10017466T/C556/632666/6901.05 (0.97–1.15)1.0067/632105/6901.16 (0.97–1.38)1.0030/63224/6900.90 (0.68–1.20)1.00196/632246/6901.12 (0.99–1.27)1.00
rs1800759C/A357/412866/9101.02 (0.92–1.12)1.0046/412126/9101.09 (0.90–1.33)1.0013/41241/9101.05 (0.75–1.48)1.00122/412320/9101.09 0.94–1.25)1.00
rs1800761G/A750/830473/4921.02 (0.93–1.12)1.00112/83060/4920.92 (0.77–1.10)1.0035/83019/4920.90 (0.66–1.22)1.00276/830166/4920.99 (0.87–1.13)1.00
rs3762894T/C839/906384/4160.98 (0.89–1.08)1.00126/90646/4160.89 (0.74–1.08)1.0038/90616/4160.89 (0.65–1.23)1.00307/906135/4160.94 (0.82–1.08)1.00
ADH7rs284787C/T739/817484/5051.06 (0.96–1.16)1.00112/81760/5050.94 (0.79–1.13)1.0029/81725/5051.18 (0.88–1.59)1.00264/817178/5051.09 (0.96–1.25)1.00
rs894369C/G832/849391/4720.92 (0.84–1.01)1.00116/84956/4720.96 (0.80–1.15)1.0042/84912/4720.75 (0.54–1.05)1.00304/849138/4720.93 (0.81–1.06)1.00
rs17588403T/A837/887386/4350.96 (0.87–1.05)1.00116/88756/4350.95 (0.79–1.14)1.0037/88717/4350.94 (0.69–1.28)1.00297/887145/4350.96 (0.84–1.10)1.00
rs1154454T/C756/808467/5140.94 (0.86–1.04)1.00117/80855/5140.80 (0.66–0.98)1.0037/80817/5140.69 (0.49–0.97)1.00260/808182/5141.00 (0.87–1.15)1.00
rs1154456T/C577/629646/6931.03 (0.94–1.13)1.0086/62986/6930.97 (0.81–1.15)1.0026/62928/6931.04 (0.78–1.40)1.00207/629235/6931.07 0.94–1.21)1.00
rs1154460G/A329/377891/9441.04 (0.95–1.15)1.0049/377123/9441.03 (0.85–1.25)1.0013/37741/9441.11 (0.80–1.55)1.00118/377322/9441.12 (0.97–1.29)1.00
rs971074G/A943/1,027280/2951.01 (0.91–1.12)1.00131/1,02741/2951.09 (0.89–1.34)1.0039/1,02715/2951.14 (0.83–1.58)1.00348/1,02794/2951.00 (0.85–1.16)1.00
rs1573496dC/G1,056/1,117166/2050.99 (0.87–1.12)1.00147/1,11725/2051.09 (0.86–1.39)1.0048/1,1176/2050.91 (0.57–1.44)1.00383/1,11759/2051.02 (0.85–1.23)1.00
ALDH2rs4767939A/G694/806528/5161.08 (0.98–1.18)1.00101/80671/5161.04 (0.87–1.25)1.0029/80625/5161.10 (0.81–1.49)1.00238/806204/5161.12 (0.98–1.28)1.00
rs2238151T/C364/482855/8371.13 (1.03–1.25)0.8451/482121/8371.18 (0.97–1.44)1.0016/48238/8371.00 (0.70–1.42)1.00117/482323/8371.24 (1.07–1.43)0.32
rs7312055G/A1,081/1,201142/1210.93 (0.78–1.12)1.00150/1,20122/1210.95 (0.67–1.34)1.0044/1,20110/1210.92 (0.57–1.50)1.00390/1,20152/1210.87 (0.67–1.12)1.00
rs2158029G/A1,166/1,26957/530.95 (0.75–1.19)1.00165/1,2697/530.76 (0.48–1.21)1.0050/1,2694/530.98 (0.52–1.82)1.00419/1,26923/530.99 (0.72–1.36)1.00
rs16941667C/T985/1,097238/2241.10 (0.98–1.23)1.00142/1,09730/2241.11 (0.88–1.40)1.0041/1,09713/2241.24 (0.88–1.75)1.00347/1,09795/2241.17 (0.99–1.37)1.00
rs16941669T/G984/1,084239/2361.06 (0.95–1.19)1.00134/1,08438/2361.20 (0.97–1.48)1.0045/1,0849/2361.00 (0.68–1.47)1.00358/1,08484/2361.10 (0.93–1.29)1.00
CYP2E1rs3813865G/C1,098/1,215125/1061.08 (0.92–1.27)1.00155/1,21517/1061.16 (0.85–1.58)1.0048/1,2156/1061.09 (0.67–1.77)1.00393/1,21549/1061.11 (0.89–1.38)1.00
rs3813867dG/C1,139/1,23783/840.97 (0.82–1.16)1.00160/1,23712/840.98 (0.70–1.38)1.0051/1,2373/840.87 (0.47–1.62)1.00405/1,23736/841.09 (0.86–1.39)1.00
rs8192772T/C1,023/1,114199/2081.07 (0.95–1.21)1.00142/1,11430/2081.09 (0.87–1.38)1.0044/1,1149/2081.11 (0.75–1.64)1.00363/1,11479/2081.14 (0.96–1.35)1.00
rs915908G/A974/1,006249/3160.93 (0.84–1.04)1.00139/1,00633/3160.92 (0.74–1.14)1.0046/1,0068/3160.77 (0.51–1.15)1.00362/1,00680/3160.87 (0.74–1.02)1.00
rs915909C/T1,164/1,27158/461.00 (0.79–1.27)1.00164/1,2717/460.88 (0.54–1.44)1.0050/1,2714/461.09 (0.60–1.99)1.00421/1,27121/460.92 (0.66–1.28)1.00
rs7092584C/T959/1,052262/2691.05 (0.95–1.17)1.00131/1,05241/2691.12 (0.91–1.38)1.0045/1,0528/2690.86 (0.58–1.28)1.00340/1,052101/2691.11 (0.96–1.30)1.00
rs743535C/T966/1,071248/2431.06 (0.95–1.19)1.00134/1,07138/2431.09 (0.88–1.35)1.0040/1,07113/2431.18 (0.84–1.66)1.00342/1,07196/2431.10 (0.94–1.29)1.00
rs2249695C/T622/682600/6390.93 (0.85–1.03)1.0087/68284/6390.93 (0.77–1.12)1.0024/68230/6390.95 (0.68–1.33)1.00223/682219/6390.93 (0.81–1.08)1.00
rs28969387A/T1,198/1,30225/200.98 (0.70–1.37)1.00170/1,3022/200.69 (0.31–1.56)1.0054/1,3020/201.00429/1,30213/201.08 (0.70–1.68)1.00
rs11101812T/C1,194/1,30026/201.11 (0.79–1.56)1.00170/1,3002/200.79 (0.35–1.77)1.0051/1,3003/201.79 (0.86–3.71)1.00427/1,30014/201.38 (0.89–2.13)1.00
Oxidative stress metabolism genes
CATrs1049982dC/T521/589700/7261.02 (0.93–1.11)1.0078/58994/7260.95 (0.80–1.14)1.0027/58926/7260.82 (0.61–1.11)1.00182/589260/7261.05 (0.92–1.19)1.00
GPX1rs8179172T/A1,172/1,27151/510.92 (0.73–1.17)1.00166/1,2716/510.86 (0.52–1.41)1.0051/1,2713/510.67 (0.32–1.39)1.00423/1,27119/510.86 (0.62–1.19)1.00
rs1800668C/T635/672588/6461.04 (0.95–1.14)1.0084/67288/6461.14 (0.96–1.35)1.0029/67225/6461.01 (0.76–1.35)1.00237/672205/6461.03 (0.91–1.17)1.00
rs3811699A/G609/649614/6731.04 (0.95–1.13)1.0077/64995/6731.16 (0.98–1.38)1.0026/64928/6731.07 (0.81–1.43)1.00230/649212/6731.02 (0.90–1.16)1.00
rs3448C/T648/729575/5931.03 (0.95–1.13)1.0096/72976/5931.02 (0.86–1.21)1.0027/72927/5931.18 (0.88–1.58)1.00222/729220/5931.12 (0.99–1.28)1.00
GPX2rs11623705G/T996/1,069227/2531.00 (0.89–1.12)1.00139/1,06933/2530.99 (0.79–1.23)1.0044/1,06910/2531.01 (0.70–1.47)1.00360/1,06982/2531.01 (0.86–1.19)1.00
rs2412065G/C694/733529/5890.94 (0.86–1.03)1.0096/73376/5890.94 (0.79–1.13)1.0032/73322/5890.81 (0.60–1.10)1.00251/733191/5890.97 (0.85–1.11)1.00
rs2737844C/T493/511725/8060.89 (0.81–0.99)1.0072/51198/8060.86 (0.71–1.04)1.0020/51134/8060.87 (0.63–1.21)1.00177/511265/8060.91 (0.80–1.05)1.00
GPX4rs757229dG/C300/358922/9631.03 (0.93–1.14)1.0039/358133/9631.08 (0.88–1.32)1.0013/35841/9630.93 (0.66–1.31)1.00103/358339/9631.04 (0.90–1.21)1.00
SOD1rs11910115A/C1,161/1,25762/650.93 (0.74–1.17)1.00165/1,2577/650.76 (0.48–1.20)1.0051/1,2573/650.80 (0.41–1.58)1.00418/1,25724/650.94 (0.69–1.30)1.00
rs4998557G/A829/959393/3601.09 (0.99–1.21)1.00123/95949/3600.98 (0.80–1.21)1.0031/95923/3601.28 (0.93–1.78)1.00288/959154/3601.17 (1.01–1.36)1.00
rs10432782T/G874/992348/3291.07 (0.97–1.18)1.00131/99241/3290.93 (0.76–1.15)1.0034/99220/3291.24 (0.90–1.71)1.00306/992136/3291.13 (0.97–1.31)1.00
rs2070424A/G1,003/1,120220/2021.06 (0.94–1.20)1.00142/1,12030/2021.02 (0.80–1.30)1.0046/1,1208/2020.85 (0.55–1.31)1.00354/1,12088/2021.09 (0.92–1.29)1.00
rs1041740C/T682/705541/6170.98 (0.90–1.07)1.0095/70577/6171.00 (0.84–1.20)1.0036/70518/6170.82 (0.60–1.12)1.00250/705192/6170.97 (0.85–1.11)1.00
SOD2rs4342445G/A752/850471/4721.11 (1.02–1.22)1.0095/85077/4721.33 (1.12–1.59)0.0942/85012/4720.84 (0.60–1.18)1.00268/850174/4721.16 (1.01–1.32)1.00
rs2842980A/T715/807508/5151.02 (0.94–1.12)1.0097/80775/5151.05 (0.88–1.25)1.0031/80723/5150.98 (0.73–1.31)1.00269/807173/5150.97 (0.85–1.10)1.00
rs8031T/A387/382836/9400.98 (0.89–1.08)1.0052/382120/9401.00 (0.83–1.21)1.0016/38238/9401.12 (0.80–1.55)1.00140/382302/9401.02 (0.89–1.17)1.00
rs5746134C/T1,125/1,25798/651.20 (0.98–1.48)1.00162/1,25710/650.98 (0.64–1.50)1.0043/1,25711/652.14 (1.25–3.67)0.34409/1,25733/651.13 (0.84–1.50)1.00
rs2758331C/A422/419801/9030.99 (0.90–1.09)1.0061/419111/9030.99 (0.82–1.20)1.0017/41937/9031.22 (0.88–1.70)1.00150/419292/9031.04 (0.91–1.20)1.00
  • aCases and controls do not sum to 1,227 and 1,325, respectively, because 4 cases and 3 controls are missing information on duration of cigarette smoking, and because a few subjects lack genotype information for some SNPs.

  • bConditional logistic regression models for estimating main effect of each SNP were conditioned on sex, race, and age category, and adjusted for continuous smoking duration rounded to whole years. ORs are for those with one or more copies of the minor allele versus the referent group of those homozygous for the major allele (dominant genetic model).

  • cBonferroni corrected for 64 statistical tests. P-values highlighted in BOLD are near statistically significant after Bonferroni correction.

  • dNot a tag SNP; included in analyses because previous studies had examined it. rs1229984 and rs1573496 have missense variants; rs3813867 and rs757229 are located 5′ near the gene; rs1049982 has a synonymous variant and is located in exon 1.

  • eSelected as a tag SNP, but had also been studied in the literature because it has a missense variant.