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. 2016 Apr 23;9:21. doi: 10.1186/s12920-016-0181-x

Table 3.

SNPs associated with mRNA expression in normal mucosa, carcinoma tissue and differential across genotypes

Tumor P-values (carcinoma) Normal P-values (normal) P-values (difference) VEP prediction
Gene SNP Model N Meanc mRNA expression Raw FDR N Mean mRNA expression Raw FDR Raw FDR
ADAR rs3766925 TT 38 831.03 0.047 0.749 36 426.06 Modifier
TA/AA 33 518.97 31 306.42
AGO2 rs7460b AA 19 284.79 0.027 0.316 18 113.50 0.021 0.267 Modifier
AT/TT 52 160.38 49 70.65
AGO2 rs1060832 CC/CT 70 191.79 66 83.06 0.050 0.403 Modifier
TT 1 326.00 1 23.00
AGO2 rs13276958 TT/TC 56 172.75 51 88.39 0.022 0.403 Modifier
CC 15 271.80 16 62.31
AGO2 rs2176397 CC/CT 66 174.39 0.043 0.316 60 78.37 Modifier
TT 5 448.20 7 114.71
AGO2 rs2271735 CC/CA 66 205.17 0.009 0.223 61 88.84 0.019 0.267 Modifier
AA 5 42.00 6 14.33
AGO2 rs2292775 GG/GA 70 191.79 66 83.06 0.049 0.403 Modifier
AA 1 326.00 1 23.00
AGO2 rs2292780 CC/CT 70 191.79 66 83.06 0.048 0.403 Modifier
TT 1 326.00 1 23.00
AGO2 rs2293939 GG/GA 65 204.00 0.039 0.316 60 85.65 Low
AA 6 81.83 7 52.29
AGO2 rs2944760 TT/TG 67 190.13 63 84.56 0.038 0.403 Modifier
GG 4 253.00 4 44.50
AGO2 rs2944761 GG 18 272.83 0.039 0.316 17 104.76 0.049 0.365 Modifier
GA/AA 53 166.79 50 74.48
AGO2 rs2977490 GG 21 161.81 0.034a 0.316 17 131.29 0.016 0.267 Modifier
GA/AA 50 207.06 50 65.46
AGO2 rs10087629 GG 22 300.91 0.005 0.223 21 115.14 0.009 0.267 Modifier
GA/AA 49 145.53 46 67.11
BMP2 rs15705 AA/AC 68 26.35 0.039 0.308 64 63.50 Modifier
CC 3 43.33 3 70.33
BMP2 rs235768 TT/TA 63 28.84 58 71.78 0.003 0.035 0.049 0.535 Moderate
AA 8 13.13 9 12.44
DCP1B rs2240610 GG/GA 52 29.46 51 12.47 0.009 0.127 Modifier
AA 19 31.79 16 29.00
DCP1B rs6489338 GG/GA 54 28.48 53 12.30 0.004 0.114 Modifier
AA 17 35.18 14 32.00
DDX5 rs1140409 AA 68 710.12 0.044 0.292 64 562.19 Moderate
AC/CC 3 212.67 3 88.33
DHX16 rs3130000 GG 60 80.68 55 63.58 0.045 0.696 Modifier
GA/AA 11 64.36 12 74.08
DICER1 rs4513027 AA/AG 65 348.18 61 286.57 0.047 0.554 Modifier
GG 6 290.00 6 64.50
DROSHA rs573010 CC 38 230.03 37 87.57 0.038 0.769 Modifier
CA/AA 33 172.42 30 108.30
DROSHA rs673019 AA 61 221.62 0.015 0.361 60 102.13 Modifier
AG/GG 10 91.20 7 51.57
DROSHA rs2330696 GG 46 224.61 40 88.18 0.008 0.470 Modifier
GA/AA 25 163.96 27 109.70
DROSHA rs3792830 AA/AG 70 200.31 0.028 0.361 66 95.74 Modifier
GG 1 409.00 1 170.00
DROSHA rs3805525 TT/TC 61 207.46 57 87.16 0.050 0.569 0.026 0.769 Modifier
CC 10 177.60 10 152.10
DROSHA rs6878195 TT 23 174.43 20 56.10 0.020 0.569 Modifier
TC/CC 48 217.06 47 114.19
DROSHA rs7719666 CC/CT 49 214.47 48 112.17 0.034 0.569 Modifier
TT 22 178.27 19 58.16
DROSHA rs10052174 AA/AG 70 200.31 0.030 0.361 66 95.74 Modifier
GG 1 409.00 1 170.00
DROSHA rs10067066 TT/TC 70 200.31 0.028 0.361 66 95.74 Modifier
CC 1 409.00 1 170.00
DROSHA rs13183642 GG 44 169.70 39 79.23 0.030 0.569 Modifier
GT/TT 27 257.93 28 121.39
DROSHA rs16901165 GG/GA 70 200.31 0.029 0.361 66 95.74 Modifier
AA 1 409.00 1 170.00
FAM57A rs2740351 AA/AG 58 42.79 54 20.30 0.006 0.089 Modifier
GG 13 24.92 13 4.54
FKBP5 rs755658 CC 59 122.02 56 179.54 0.042 0.232 Modifier
CT/TT 12 82.50 11 69.09
GEMIN4 rs7813 AA/AG 58 59.29 54 32.72 0.023 0.113 Modifier
GG 13 28.62 13 8.69
GEMIN4 rs2740348 CC 51 64.31 47 35.26 0.013 0.089 Moderate
CG/GG 20 26.55 20 11.15
GEMIN4 rs2740349 TT 51 64.31 0.005 0.047 47 35.26 0.012 0.089 Moderate
TC/CC 20 26.55 20 11.15
MAPK1 rs743409 GG/GA 60 280.25 56 201.55 0.032 0.979 Modifier
AA 11 341.64 11 126.00
MAPK14 rs8510 CC 60 246.67 56 147.52 0.016 0.157 Modifier
CT/TT 11 193.64 11 62.91
PRKRA rs2059691b GG 33 48.67 0.044a 0.428 30 15.37 0.000 0.003 Modifier
GA/AA 38 89.16 37 51.24
RBBP6 rs2033214 TT 58 200.36 56 130.27 0.038 0.418 Modifier
TG/GG 13 119.23 11 51.00
SKIV2L rs449643 CC 52 73.13 0.016 0.458 50 51.50 Moderate
CT/TT 19 136.58 17 95.35
TARBP2 rs34649330 CC/CT 69 22.33 0.037 0.685 65 10.69 0.024 0.640 Modifier
TT 2 51.50 2 10.00
TNRC6A rs1030211 AA 56 266.98 0.044 0.299 55 228.71 Modifier
AG/GG 15 189.33 12 138.83
TNRC6A rs4788430 GG 41 298.59 0.010 0.212 39 252.33 Modifier
GA/AA 30 184.97 28 157.29
TNRC6A rs6497755 AA 23 316.39 0.030 0.299 22 303.50 0.009 0.194 Modifier
AC/CC 48 219.04 45 168.18
XPO5 rs11077 TT/TG 57 178.12 55 70.96 0.017 0.157 Modifier
GG 14 328.86 12 134.83
XPO5 rs1106841 AA/AC 59 183.85 57 73.46 0.036 0.232 Low
CC 12 325.83 10 133.40
XPO5 rs2257082 GG/GA 66 208.95 62 75.56 0.012 0.157 Low
AA 5 193.20 5 167.20

a This p-value is for the recessive model

b This mRNA was significantly differentially expressed across genotypes using both the recessive and dominant models

c Means are displayed in count data (rather than RPKMs)