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Table 4 Comparison of allele frequencies (additive model), as tested by chi-square analysis and permutations test, of individual tag-SNPs, HS vs. HR Caucasian-only sample (N = 196)

From: Head-and-neck squamous cell carcinoma risk in smokers: no association detected between phenotype and AHR, CYP1A1, CYP1A2, or CYP1B1 genotype

Gene

Tag-SNP #

SNP ID

Asso-ciated allelea

Cases (HS) allele frequencies

Controls (HR) allele frequencies

P value (chi-square analysis)

P value, following 100 K permutations

AHR

1

rs62444550

A

0.926

0.884

0.1598

0.741

AHR

2

AHR10SNP

A

0.431

0.416

0.7654

1.00

AHR

3

rs10250822

C

0.282

0.205

0.0768

0.4705

AHR

4

rs4719497

C

0.188

0.100

0.0134 *

0.1048

AHR

5

rs3757824

T

0.856

0.795

0.1069

0.6213

AHR

7

rs713150

G

0.272

0.205

0.1204

0.6554

AHR

8

rs17722841

G

0.797

0.795

0.9551

1.00

AHR

9

rs2282885

A

0.629

0.579

0.3139

0.9577

AHR

10

rs2282883

T

0.386

0.337

0.3102

0.9496

AHR

11

rs4236290

T

0.896

0.868

0.3958

0.9802

AHR

12

rs2158041

T

0.267

0.221

0.287

0.9119

AHR

13

rs3802082

A

0.876

0.842

0.3308

0.9603

AHR

14

rs7811989

A

0.302

0.263

0.3939

0.9776

AHR

15

rs2074113

G

0.941

0.921

0.4452

0.992

AHR

16

rs2066853

A

0.084

0.079

0.8506

1.00

CYP1A1

1

rs4646903

G

0.104

0.084

0.5039

0.9866

CYP1A1

2

rs2606345

C

0.351

0.337

0.7604

0.9999

CYP1A1

3

rs3826042

C

0.955

0.937

0.4136

0.9446

CYP1A1

4

rs7495708

C

0.158

0.153

0.8745

1.00

CYP1A2

1

rs2069514

A

0.035

0.016

0.2365

0.8158

CYP1A2

2

rs762551

C

0.292

0.279

0.7736

1.00

CYP1A2

3

rs2470890

C

0.386

0.332

0.2606

0.8355

CYP1A2

4

rs17861162

G

0.064

0.037

0.216

0.7605

CYP1B1

1

rs162562

G

0.282

0.221

0.1639

0.6189

CYP1B1

2

rs1800440

T

0.856

0.821

0.3404

0.8777

CYP1B1

3

rs1056837

G

0.545

0.542

0.9612

1.00

CYP1B1

4

rs1056836

C

0.460

0.458

0.9604

1.00

CYP1B1

5

rs1056827

A

0.297

0.268

0.5298

0.9853

CYP1B1

6

rs10012

C

0.302

0.263

0.3939

0.9263

CYP1B1

7

rs162558

T

0.812

0.763

0.238

0.751

CYP1B1

8

rs2855655

C

0.589

0.547

0.4043

0.9302

CYP1B1

9

rs162557

A

0.277

0.242

0.4283

0.9473

CYP1B1

10

rs162556

A

0.540

0.516

0.6369

0.9954

CYP1B1

11

rs162555

T

0.817

0.774

0.2895

0.8232

CYP1B1

12

rs10175368

T

0.277

0.258

0.6658

0.9985

  1. * Statistically significant (P < 0.05)
  2. aAssociated allele, as selected by the HaploView program