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Table 2 Association results of SNPs in the GWAS with all patients, and subgroup analysis

From: Genome-wide association study identifies genetic susceptibility loci and pathways of radiation-induced acute oral mucositis

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
  1. Case, RTOG grade ≥ 3; Control, RTOG grade ≤ 2
  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
  3. aThe subgroup of patients who received intensity modulated radiation therapy
  4. bThe subgroup of patients who received two-dimensional conventional radiotherapy