Table 2.
Association results of SNPs in the GWAS with all patients, and subgroup analysis
| SNP | Locus | CHR | MA | GENE | All patients | |||
|---|---|---|---|---|---|---|---|---|
| N | OR (95% CI) | P | MAF (case/control) | |||||
| rs9484606 | 15 | 6 | C | VTA1/ADGRG6 | 1454 | 1.70 (1.36–2.13) | 2.98 × 10−6 | 0.25/0.18 |
| rs16876733 | 17 | 7 | C | PER4/NDUFA4 | 1452 | 1.95 (1.47–2.59) | 3.05 × 10−6 | 0.16/0.09 |
| rs117157809 | 21 | 8 | C | TNKS | 1423 | 3.72 (2.10–6.57) | 6.33 × 10−6 | 0.05/0.01 |
| rs4433399 | 1 | 1 | A | MIR4417/MIR4689 | 1449 | 1.69 (1.34–2.12) | 8.53 × 10−6 | 0.23/0.16 |
| rs3094972 | 18 | 7 | T | STEAP1B | 1460 | 0.46 (0.32–0.65) | 1.33 × 10−5 | 0.07/0.12 |
| rs11908263 | 49 | 20 | A | BTBD3/LOC101929486 | 1450 | 2.06 (1.49–2.86) | 1.36 × 10−5 | 0.11/0.07 |
| rs1562525 | 5 | 3 | A | FHIT | 1467 | 1.75 (1.36–2.25) | 1.39 × 10−5 | 0.18/0.12 |
| rs9941163 | 43 | 16 | T | GOT2/APOOP5 | 1447 | 2.56 (1.67–3.93) | 1.72 × 10−5 | 0.07/0.03 |
| rs59936027 | 35 | 13 | A | WBP4/MIR3168 | 1439 | 1.61 (1.29–2.00) | 2.19 × 10−5 | 0.26/0.18 |
| rs7673990 | 10 | 4 | G | TENM3 | 1455 | 1.81 (1.38–2.38) | 2.22 × 10−5 | 0.15/0.09 |
| rs13227327 | 16 | 7 | A | SDK1 | 1417 | 1.62(1.30-2.03) | 2.24 × 10−5 | 0.27/0.19 |
| rs561697 | 44 | 18 | G | LINC00907 | 1420 | 1.71 (1.33–2.19) | 2.49 × 10−5 | 0.20/0.14 |
| rs10957542 | 22 | 8 | T | EYA1 | 1433 | 0.42 (0.28–0.63) | 3.08 × 10−5 | 0.05/0.09 |
| rs6133617 | 48 | 20 | T | PLCB1 | 1456 | 1.49 (1.23–1.79) | 3.11 × 10−5 | 0.55/0.46 |
| rs1079866 | 19 | 7 | G | LINC01449/INHBA | 1465 | 1.59 (1.28–1.98) | 3.19 × 10−5 | 0.26/0.19 |
| rs9570470 | 36 | 13 | A | LINC00378/MIR3169 | 1461 | 0.50 (0.36–0.70) | 3.28 × 10−5 | 0.07/0.13 |
| rs7068532 | 29 | 10 | A | DHTKD1 | 1446 | 1.60(1.28-2.00) | 3.33 × 10−5 | 0.26/0.19 |
| rs4909632 | 24 | 8 | G | KHDRBS3/LOC101927915 | 1447 | 1.49 (1.24–1.80) | 3.46 × 10−5 | 0.56/0.48 |
| rs12430962 | 37 | 13 | A | SNORA107/LINC00375 | 1461 | 0.64 (0.52–0.79) | 3.96 × 10−5 | 0.22/0.30 |
| rs138519422 | 40 | 15 | C | OTUD7A/CHRNA7 | 1415 | 3.14 (1.81–5.43) | 4.52 × 10−5 | 0.05/0.02 |
| rs6814005 | 8 | 4 | T | MAPK10 | 1461 | 2.34 (1.55–3.53) | 5.16 × 10−5 | 0.07/0.03 |
| rs80231193 | 27 | 9 | C | LHX2/NEK6 | 1421 | 2.79 (1.70–4.60) | 5.41 × 10−5 | 0.05/0.02 |
| rs10816756 | 26 | 9 | C | IKBKAP | 1464 | 1.87 (1.38–2.53) | 5.77 × 10−5 | 0.12/0.07 |
| rs7147736 | 38 | 14 | A | LINC00645/FOXG1-AS1 | 1420 | 1.77 (1.34–2.33) | 5.99 × 10−5 | 0.16/0.11 |
| rs79945158 | 2 | 1 | A | LOC100996251 | 1423 | 3.39 (1.87–6.16) | 6.06 × 10−5 | 0.04/0.02 |
| rs79549170 | 31 | 12 | G | GNPTAB/DRAM1 | 1439 | 1.98 (1.42–2.77) | 6.13 × 10−5 | 0.10/0.06 |
| rs17143701 | 28 | 10 | C | LINC00708/LOC105755953 | 1463 | 1.86 (1.37–2.51) | 6.46 × 10−5 | 0.12/0.07 |
| rs79052434 | 41 | 15 | G | DPH6-AS1 | 1459 | 0.50 (0.36–0.70) | 6.76 × 10−5 | 0.07/0.12 |
| rs2850108 | 50 | 21 | A | CLDN14 | 1452 | 1.48 (1.22–1.79) | 7.11 × 10−5 | 0.43/0.34 |
| rs7742301 | 13 | 6 | T | CASC6/EPHA7 | 1467 | 1.62 (1.28–2.05) | 7.25 × 10−5 | 0.21/0.15 |
| rs16987032 | 47 | 19 | A | GALP | 1467 | 1.66 (1.29–2.13) | 7.59 × 10−5 | 0.18/0.12 |
| rs28375758 | 12 | 5 | C | KIF4B/SGCD | 1456 | 1.59 (1.26–2.01) | 8.78 × 10−5 | 0.24/0.18 |
| rs36058653 | 46 | 18 | G | ZNF407/ZADH2 | 1437 | 1.65 (1.28–2.11) | 9.06 × 10−5 | 0.19/0.13 |
| rs76156855 | 32 | 12 | T | GPR133 | 1444 | 3.69 (1.92–7.10) | 9.10 × 10−5 | 0.03/0.01 |
| rs9752986 | 4 | 2 | T | KCNH7/FIGN | 1433 | 2.07 (1.43–2.98) | 9.79 × 10−5 | 0.09/0.05 |
| rs10050575 | 11 | 5 | A | C5orf66 | 1421 | 3.48 (1.86–6.53) | 9.85 × 10−5 | 0.04/0.01 |
| SNP | IMRTa | 2D-CRTb | ||||||
|---|---|---|---|---|---|---|---|---|
| N | OR (95% CI) | P | MAF (case/control) | N | OR (95% CI) | P | MAF (case/control) | |
| rs9484606 | 707 | 1.38 (1.20–1.59) | 2.70 × 10−2 | 0.22/0.17 | 747 | 2.45 (2.03–2.96) | 2.14 × 10−6 | 0.31/0.19 |
| rs16876733 | 699 | 2.02 (1.69–2.42) | 6.56 × 10−5 | 0.17/0.10 | 753 | 1.79 (1.39–2.30) | 2.10 × 10−2 | 0.13/0.09 |
| rs117157809 | 704 | 3.34 (2.31–4.84) | 1.10 × 10−3 | 0.04/0.01 | 719 | 5.06 (3.13–8.18) | 6.99 × 10−4 | 0.05/0.02 |
| rs4433399 | 696 | 1.74 (1.50–2.02) | 2.73 × 10−4 | 0.22/0.14 | 753 | 1.64 (1.36–1.98) | 1.01 × 10−2 | 0.25/0.17 |
| rs3094972 | 708 | 0.42 (0.33–0.53) | 1.06 × 10−4 | 0.06/0.13 | 752 | 0.49 (0.36–0.66) | 1.75 × 10−2 | 0.07/0.10 |
| rs11908263 | 707 | 1.88 (1.51–2.34) | 3.89 × 10−3 | 0.10/0.06 | 743 | 2.27 (1.75–2.94) | 1.65 × 10−3 | 0.15/0.07 |
| rs1562525 | 714 | 1.92 (1.62–2.28) | 9.15 × 10−5 | 0.18/0.11 | 753 | 1.51 (1.22–1.86) | 4.92 × 10−2 | 0.18/0.13 |
| rs9941163 | 709 | 2.58 (1.95–3.41) | 6.85 × 10−4 | 0.07/0.03 | 738 | 2.08 (1.45–2.98) | 4.14 × 10−2 | 0.06/0.03 |
| rs59936027 | 709 | 1.49 (1.30–1.71) | 4.41 × 10−3 | 0.26/0.20 | 730 | 1.85 (1.53–2.24) | 1.30 × 10−3 | 0.26/0.18 |
| rs7673990 | 710 | 1.64 (1.37–1.96) | 5.96 × 10−3 | 0.13/0.09 | 745 | 2.02 (1.60–2.54) | 1.87 × 10−3 | 0.17/0.09 |
| rs13227327 | 682 | 1.44 (1.25–1.66) | 1.10 × 10−2 | 0.27/0.21 | 735 | 2.04 (1.69–2.47) | 1.87 × 10−4 | 0.29/0.18 |
| rs561697 | 682 | 1.69 (1.44–1.98) | 8.13 × 10−4 | 0.20/0.13 | 738 | 1.77 (1.42–2.21) | 8.31 × 10−3 | 0.21/0.14 |
| rs10957542 | 693 | 0.44 (0.34–0.56) | 1.10 × 10−3 | 0.05/0.10 | 740 | 0.39 (0.27–0.56) | 8.98 × 10−3 | 0.04/0.09 |
| rs6133617 | 708 | 1.53 (1.36–1.73) | 4.10 × 10−4 | 0.54/0.45 | 748 | 1.45 (1.24–1.70) | 1.97 × 10−2 | 0.56/0.46 |
| rs1079866 | 714 | 1.68 (1.46–1.93) | 2.26 × 10−4 | 0.27/0.18 | 751 | 1.54 (1.27–1.86) | 2.28 × 10−2 | 0.26/0.20 |
| rs9570470 | 708 | 0.50 (0.41–0.61) | 7.73 × 10−4 | 0.07/0.13 | 753 | 0.51 (0.38–0.68) | 1.95 × 10−2 | 0.07/0.14 |
| rs7068532 | 702 | 1.66 (1.44–1.91) | 3.47 × 10−4 | 0.26/0.18 | 744 | 1.47 (1.22–1.78) | 4.34 × 10−2 | 0.24/0.20 |
| rs4909632 | 706 | 1.40 (1.24–1.58) | 6.09 × 10−3 | 0.53/0.46 | 741 | 1.67 (1.42–1.96) | 1.80 × 10−3 | 0.62/0.50 |
| rs12430962 | 708 | 0.66 (0.58–0.75) | 2.09 × 10−3 | 0.23/0.31 | 753 | 0.60 (0.50–0.73) | 8.88 × 10−3 | 0.21/0.29 |
| rs138519422 | 697 | 3.38 (2.33–4.89) | 1.14 × 10−3 | 0.05/0.01 | 718 | 2.65 (1.69–4.16) | 2.87 × 10−2 | 0.05/0.02 |
| rs6814005 | 711 | 2.27 (1.75–2.94) | 1.54 × 10−3 | 0.08/0.03 | 750 | 2.49 (1.72–3.60) | 1.40 × 10−2 | 0.06/0.03 |
| rs80231193 | 705 | 3.01 (2.14–4.23) | 1.05 × 10−3 | 0.05/0.02 | 716 | 2.98 (1.98–4.49) | 7.81 × 10−3 | 0.06/0.03 |
| rs10816756 | 711 | 1.80 (1.49–2.18) | 1.97 × 10−3 | 0.12/0.07 | 753 | 2.12 (1.62–2.78) | 6.30 × 10−3 | 0.11/0.07 |
| rs7147736 | 683 | 1.82 (1.52–2.18) | 9.13 × 10−4 | 0.16/0.10 | 737 | 1.67 (1.31–2.12) | 2.92 × 10−2 | 0.15/0.12 |
| rs79945158 | 688 | 2.59 (1.75–3.83) | 1.57 × 10−2 | 0.03/0.02 | 735 | 5.92 (3.66–9.57) | 2.29 × 10−4 | 0.05/0.02 |
| rs79549170 | 697 | 1.67 (1.34–2.08) | 2.05 × 10−2 | 0.09/0.06 | 742 | 2.64 (2.02–3.46) | 3.58 × 10−4 | 0.12/0.06 |
| rs17143701 | 713 | 1.97 (1.61–2.41) | 7.27 × 10−4 | 0.12/0.07 | 750 | 1.74 (1.36–2.23) | 2.81 × 10−2 | 0.13/0.08 |
| rs79052434 | 711 | 0.51 (0.41–0.64) | 1.72 × 10−3 | 0.07/0.12 | 748 | 0.51 (0.38–0.68) | 2.05 × 10−2 | 0.07/0.13 |
| rs2850108 | 700 | 1.38 (1.22–1.56) | 9.09 × 10−3 | 0.39/0.32 | 752 | 1.64 (1.40–1.92) | 2.55 × 10−3 | 0.49/0.36 |
| rs7742301 | 714 | 1.54 (1.33–1.79) | 4.29 × 10−3 | 0.20/0.15 | 753 | 1.64 (1.34–2.00) | 1.47 × 10−2 | 0.24/0.14 |
| rs16987032 | 714 | 1.37 (1.17–1.61) | 4.69 × 10−2 | 0.17/0.14 | 753 | 2.41 (1.95–2.97) | 4.19 × 10−5 | 0.21/0.11 |
| rs28375758 | 704 | 1.37 (1.18–1.59) | 3.72 × 10−2 | 0.22/0.19 | 752 | 2.07 (1.69–2.53) | 2.22 × 10−4 | 0.27/0.18 |
| rs36058653 | 702 | 1.54 (1.31–1.81) | 6.13 × 10−3 | 0.18/0.13 | 735 | 2.09 (1.68–2.60) | 8.54 × 10−4 | 0.20/0.13 |
| rs76156855 | 704 | 4.29 (2.82–6.53) | 4.66 × 10−4 | 0.04/0.01 | 740 | 3.91 (2.06–7.42) | 3.24 × 10−2 | 0.02/0.01 |
| rs9752986 | 688 | 1.93 (1.52–2.45) | 5.92 × 10−3 | 0.09/0.04 | 745 | 2.27 (1.68–3.06) | 6.91 × 10−3 | 0.10/0.05 |
| rs10050575 | 688 | 2.61 (1.75–3.89) | 1.67 × 10−2 | 0.03/0.01 | 733 | 5.79 (3.48–9.64) | 5.37 × 10−4 | 0.04/0.01 |
Case, RTOG grade ≥ 3; Control, RTOG grade ≤ 2
SNP, single nucleotide polymorphism; CHR, chromosome; MA, minor allele; MAF, minor allele frequency; OR, odds ratio for minor allele; 95% CI, 95% confidence interval
aThe subgroup of patients who received intensity modulated radiation therapy
bThe subgroup of patients who received two-dimensional conventional radiotherapy