Table 3. Association of variants and genes with HBV associated with HCC.
| Gene symbol | Associated SNVs | Variant level OR | Variant level P-value (FDR adjusted) | Numbers of SNVs | SKAT-O gene level P-value (FDR adjusted) | |||
|---|---|---|---|---|---|---|---|---|
| HCC compared with HC | HCC compared with SH | HCC compared with HC | HCC compared with SH | HCC compared with HC | HCC compared with SH | |||
| HLA-B | rs2596493 | Inf | Inf | 2.25E-18 | 3.59E-18 | 106 | 1.7232E-16 | 2.67597E-10 |
| HLA-B | rs1131285 | Inf | Inf | 1.7E-13 | 1.13E-13 | 106 | 1.7232E-16 | 2.67597E-10 |
| HLA-B | rs1065386 | Inf | Inf | 6.97E-09 | 6.97E-09 | 106 | 1.7232E-16 | 2.67597E-10 |
| HLA-B | rs1050570 | Inf | Inf | 1.87E-08 | 1.83E-08 | 106 | 1.7232E-16 | 2.67597E-10 |
| HLA-B | rs1050556 | Inf | Inf | 0.0000019 | 0.0000019 | 106 | 1.7232E-16 | 2.67597E-10 |
| HLA-B | rs1131215 | Inf | Inf | 0.0000623 | 0.0000619 | 106 | 1.7232E-16 | 2.67597E-10 |
| HLA-C | rs41556617 | Inf | Inf | 7.92E-12 | 6.79E-12 | 108 | 5.33706E-07 | 3.14762E-05 |
| HLA-C | rs2308527 | Inf | Inf | 0.000000801 | 0.00000074 | 108 | 5.33706E-07 | 3.14762E-05 |
| HLA-DPA1 | rs1042174 | 16.63 | 28.69 | 0.000000899 | 3.15E-08 | 33 | 1.4521E-08 | 4.3979E-07 |
| HLA-DPA1 | rs1126543 | Inf | Inf | 2.9E-09 | 2.9E-09 | 33 | 1.4521E-08 | 4.3979E-07 |
| HLA-DPA1 | rs2308930 | Inf | Inf | 6.97E-09 | 6.97E-09 | 33 | 1.4521E-08 | 4.3979E-07 |
| HLA-DPA1 | rs2308929 | Inf | Inf | 6.97E-09 | 6.97E-09 | 33 | 1.4521E-08 | 4.3979E-07 |
| HLA-DPA1 | rs1126542 | Inf | Inf | 1.87E-08 | 1.83E-08 | 33 | 1.4521E-08 | 4.3979E-07 |
| HLA-DQA1 | rs9272896 | Inf | Inf | 0.0000116 | 0.0000113 | 81 | 3.33767E-07 | 1.30562E-05 |
| HLA-DQB1 | rs1049055 | 36.19 | 75.53 | 2.7E-11 | 6.3E-14 | 110 | 9.04603E-10 | 7.65036E-10 |
| HLA-DQB1 | rs1130430 | 19.53322682 | 11.3 | 0.00000465 | 0.0000835 | 110 | 9.04603E-10 | 7.65036E-10 |
| HLA-DQB1 | rs1049057 | Inf | Inf | 4.67E-08 | 4.18E-08 | 110 | 9.04603E-10 | 7.65036E-10 |
| HLA-DQB1 | rs1063345 | Inf | Inf | 0.00000465 | 0.0000045 | 110 | 9.04603E-10 | 7.65036E-10 |
| HLA-DQB1 | rs1140316 | Inf | Inf | 0.0000623 | 0.0000619 | 110 | 9.04603E-10 | 7.65036E-10 |
| HLA-DQB2 | rs9276572 | Inf | Inf | 2.05E-15 | 2.05E-15 | 21 | 5.04185E-06 | 0.000688766 |
| HLA-DRB1 | rs17211105 | 18.48 | 18.48 | 3.21E-08 | 3.02E-08 | 126 | 1.08223E-14 | 1.74002E-11 |
| HLA-DRB1 | rs9270299 | 12.56 | 16.04 | 0.00000974 | 0.00000051 | 126 | 1.08223E-14 | 1.74002E-11 |
| HLA-DRB1 | rs17883134 | 44.09 | 20.97 | 1.07E-10 | 1.83E-08 | 126 | 1.08223E-14 | 1.74002E-11 |
| HLA-DRB1 | rs9270303 | 20.97 | 20.97 | 1.95E-08 | 1.83E-08 | 126 | 1.08223E-14 | 1.74002E-11 |
| HLA-DRB1 | rs2308759 | 353.69 | 214.66 | 5.04E-20 | 3.59E-18 | 126 | 1.08223E-14 | 1.74002E-11 |
| HLA-DRB1 | rs17211091 | 18.04 | 96.28 | 0.000000363 | 1.61E-10 | 126 | 1.08223E-14 | 1.74002E-11 |
| HLA-DRB1 | rs113734598 | 48.46 | 15.62 | 0.00000159 | 0.0000619 | 126 | 1.08223E-14 | 1.74002E-11 |
| HLA-DRB1 | rs9269693 | 136.13 | Inf | 9.53E-13 | 3.74E-14 | 126 | 1.08223E-14 | 1.74002E-11 |
| HLA-DRB1 | rs1064697 | Inf | Inf | 0.000000124 | 0.000000107 | 126 | 1.08223E-14 | 1.74002E-11 |
| HLA-DRB1 | rs1071752 | Inf | Inf | 0.0000623 | 0.0000619 | 126 | 1.08223E-14 | 1.74002E-11 |
| HLA-DRB5 | rs17211043 | Inf | Inf | 0.000000124 | 0.000000107 | 83 | 4.77962E-10 | 2.52675E-06 |
| HLA-DRB5 | rs77853982 | Inf | Inf | 0.000000801 | 0.00000074 | 83 | 4.77962E-10 | 2.52675E-06 |
| HLA-DRB5 | rs701884 | 38.71 | Inf | 0.0000245 | 0.0000019 | 83 | 4.77962E-10 | 2.52675E-06 |
| HLA-DRB5 | rs1064587 | 35.87 | Inf | 0.000058 | 0.0000045 | 83 | 4.77962E-10 | 2.52675E-06 |
| HCAR2 | rs579877 | Inf | Inf | 0.0000277 | 0.000027 | 11 | 2.03163E-06 | 3.36441E-05 |
| HCAR2 | rs579876 | Inf | Inf | 0.0000277 | 0.000027 | 11 | 2.03163E-06 | 3.36441E-05 |
| NLRP11 | NM_145007: c.*131_*130delTG | 9.684525939 | 14.70656392 | 2.71228E-05 | 6.95927E-07 | 22 | 6.83802E-07 | 2.97726E-09 |
| NLRP11 | rs368692979 | 17.64443693 | 32.53501457 | 8.81316E-08 | 8.54585E-10 | 22 | 6.83802E-07 | 2.97726E-09 |
| RAET1E | NM_139165: exon5:c.623-2- >TT | 16.6900097 | 20.59517629 | 1.0742E-07 | 9.68061E-09 | 21 | 0.000603407 | 3.07916E-05 |
Abbreviations: Inf, infinite; HCAR2, hydroxy-carboxylic acid receptor 2; OR, odds ratio; NLRP11, NLR protein 11; RAET1E, retinoic acid early transcript 1E; SH, self-healing cases with previous HBV infection.