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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