Table 4.
Haplotype associations.
| Variable | BP1 | BP2 | SNP1 | SNP2 | Haplotype | F | Beta | T | P | Genes |
|---|---|---|---|---|---|---|---|---|---|---|
| HBV | 30443533 | 30471924 | rs3129808 | rs3130113 | AGCAAAGAAGA | 0.096 | −1.32 | 12.8 | 5.00E–04 | RPP21 |
| HBV | 31920017 | 31956199 | rs9267576 | rs589428 | CGGTCGGGACA | 0.0813 | −1.66 | 20.3 | 1.00E–04 | C6orf48|NEU1|C6orf29|BAT8 |
| HBV | 31959213 | 31978305 | rs652888 | rs558702 | GGAGA | 0.072 | −1.55 | 14.6 | 5.00E–04 | BAT8|ZBTB12 |
| HBV | 31980530 | 32002605 | rs2763982 | rs3020644 | GAAGA | 0.156 | −1.06 | 14.4 | 5.00E–04 | ZBTB12|C2 |
| HBV | 32024379 | 32036778 | rs537160 | rs419788 | AGGAGA | 0.0784 | −1.54 | 16.7 | 3.00E–04 | BF|RDBP|SKIV2L |
| HBV | 32134085 | 32174155 | rs1009382 | rs17421624 | AGCGAGGA | 0.0761 | −1.55 | 16.4 | 3.00E–04 | TNXB |
| HBV | 32274362 | 32290737 | rs8192575 | rs206015 | CAAGGACGTGG | 0.111 | −1.1 | 11.8 | 0.0009999 | NOTCH4 |
| HBV | 32298006 | 32302832 | rs3132946 | rs3096691 | GGGGAG | 0.216 | −0.819 | 12.7 | 4.00E–04 | NOTCH4 |
| HBV | 32303966 | 32306914 | rs365053 | rs2849015 | AAAAA | 0.116 | −1.37 | 19.1 | 1.00E–04 | NOTCH4 |
| HBV | 32315371 | 32319295 | rs416352 | rs411326 | AAAAG | 0.0728 | −1.56 | 14.7 | 5.00E–04 | NOTCH4 |
| PnPS4 | 32871088 | 32888702 | rs2621377 | rs11244 | GCACGAAAGGAGG | 0.325 | 0.691 | 12.9 | 0.0007999 | HLA-DOB |
| PnPS18C | 29816201 | 29836188 | rs1610603 | rs1610628 | GGAAAA | 0.012 | −3.22 | 13 | 0.0005999 | FLJ35429 |
| PnPS19F | 33252221 | 33293896 | rs1799908 | rs213212 | AAGGGCAAACGCGAGAGAGGGGA | 0.0701 | 1.71 | 16.4 | 0.0006999 | COL11A2|RXRB|SLC39A7|HSD17B8|RING1 |
| PnPS23F | 32263559 | 32272847 | rs204993 | rs2071280 | AAACGG | 0.287 | −1.12 | 13.6 | 3.00E–04 | PBX2|GPSM3|NOTCH4 |
| IgG | 29807135 | 29811241 | rs2523402 | rs2394160 | AGGAGGGAA | 0.201 | −0.34 | 14.3 | 0.0005999 | FLJ35429 |
| IgG | 29816201 | 29836188 | rs1610603 | rs1610628 | GGGGAA | 0.216 | −0.376 | 17.4 | 2.00E–04 | FLJ35429 |
| IgG | 31133030 | 31183094 | rs2523849 | rs1064190 | AGGGAAGAGGGCAAGCA | 0.164 | 0.343 | 11.7 | 0.0009999 | C6orf15 |
| IgG | 31601867 | 31630648 | rs2734574 | rs6929796 | TCACAAGAGGCAAGTGGCG | 0.0224 | 0.84 | 12.3 | 0.0009999 | BAT1|ATP6V1G2|NFKBIL1 |
| IgG1 | 29816201 | 29836188 | rs1610603 | rs1610628 | GGGGAA | 0.216 | −0.425 | 16.5 | 5.00E–04 | FLJ35429 |
| IgG2 | 30253719 | 30320795 | rs7774730 | rs3094635 | CCGGGACAGGGGAAGGGACGAAGGGCGAT | 0.0243 | 1.69 | 15.7 | 2.00E–04 | TRIM15|TRIM26|FLJ45422 |
| IgG4 | 31133030 | 31183094 | rs2523849 | rs1064190 | AGGGAAGAGAGCGAGCA | 0.068 | 2.2 | 12.7 | 4.00E–04 | C6orf15 |
| IgG4 | 32491419 | 32497626 | rs3135382 | rs3135363 | AAA | 0.736 | −1.43 | 11.8 | 5.00E–04 | BTNL2 |
| IgM | 28983481 | 29023087 | rs209122 | rs763009 | GGACAGGGGGTTGA | 0.426 | 0.333 | 17.3 | 1.00E–04 | RFP |
| IgM | 28983481 | 29023087 | rs209122 | rs763009 | AGGCTAGAAGAAGG | 0.0766 | −0.581 | 12.5 | 0.0007999 | RFP |
| IgM | 29054899 | 29207558 | rs3135322 | rs3130778 | GGAGCAGAAACGAAAAAAGCAGGAAAACAAGATAGAGAAAAG | 0.076 | −0.59 | 13.2 | 0.0007999 | RFP|OR2W1|OR2B3|OR2J3 |
| IgM | 29216270 | 29364399 | rs9393945 | rs1884123 | GCCAAAGAACAGGAAGAGAAGGAACGGAGAGAGG | 0.419 | 0.294 | 12.4 | 4.00E–04 | OR2J3|OR2J2|OR5U1 |
| IgM | 29216270 | 29364399 | rs9393945 | rs1884123 | GGAGGAACGGGAACGAAGGGAACCACAGGGAGGA | 0.076 | −0.584 | 12.7 | 0.0007999 | OR2J3|OR2J2|OR5U1 |
| IgM | 29390330 | 29443516 | rs9393954 | rs9380120 | AATGAACAAGA | 0.115 | −0.436 | 11.2 | 0.0009999 | OR5U1|OR5V1|OR12D3 |
| IgM | 29444033 | 29455023 | rs4713211 | rs238880 | AAGGGA | 0.444 | 0.274 | 11.7 | 0.0008999 | OR12D3 |
| IgM | 29519411 | 29576788 | rs1535039 | rs1233487 | GAGGGGGAGAGGAAGACAAAG | 0.0717 | −0.571 | 11.5 | 0.0009999 | OR10C1|OR2H1|MAS1L |
| IgM | 29580895 | 29591947 | rs757256 | rs1592410 | AAAGA | 0.212 | −0.41 | 16 | 2.00E–04 | MAS1L |
| IgM | 29807135 | 29811241 | rs2523402 | rs2394160 | AGGAGGGAA | 0.201 | −0.349 | 11.7 | 5.00E–04 | FLJ35429 |
| IgM | 29926641 | 29931006 | rs2734985 | rs2428510 | GAAA | 0.175 | −0.387 | 12.3 | 0.0005999 | HLA-G |
| IgM | 30017786 | 30028444 | rs3094141 | rs1655912 | CGCAAC | 0.194 | −0.352 | 12.3 | 0.0007999 | HLA-A |
| IgM | 30059085 | 30119560 | rs2735067 | rs259939 | GCAGAAACCGCACG | 0.132 | −0.498 | 15 | 2.00E–04 | HCG9|ZNRD1 |
| IgM | 30344733 | 30424718 | rs2844762 | rs9380174 | GACAGGTGCAACGGTAATGGGAAAAAAATG | 0.072 | −0.592 | 12.3 | 2.00E–04 | FLJ45422|TRIM39|RPP21 |
| IgM | 31133030 | 31183094 | rs2523849 | rs1064190 | AAGGGGAGAGAAAAGCA | 0.092 | −0.529 | 13.7 | 5.00E–04 | C6orf15 |
BP1: physical position of left-most (5’) SNP (base-pair). BP2: Physical position of right-most (3’) SNP (base-pair). SNP1: left-most (5’) SNP. SNP2: left-most (3’) SNP. F: frequency. BETA (OR): regression coefficient (estimated odds ratio). T: test statistic (T from Wald test). P: empirical p-values from permutation procedures (10,000 permutations). Haplotypes containing SNPs that are individually associated with immune responses are shown in bold.