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Table 3 SNPs associated with mRNA expression in normal mucosa, carcinoma tissue and differential across genotypes

From: Impact of polymorphisms in microRNA biogenesis genes on colon cancer risk and microRNA expression levels: a population-based, case-control study

  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      
  1. a This p-value is for the recessive model
  2. b This mRNA was significantly differentially expressed across genotypes using both the recessive and dominant models
  3. c Means are displayed in count data (rather than RPKMs)