Skip to main content

Table 6 Comparison of haplotype frequencies (additive model), as tested by chi-square analysis and permutations test, 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

Haploblock and inferred haplotypes

Haplotype total frequency

Cases (HS) frequencies

Controls (HR) frequencies

P value (chi-square analysis)

P value, following 100 K permutations

AHR Block 1

 ACTTTC

0.477

0.485

0.468

0.7405

1.00

 AATTCC

0.173

0.144

0.205

0.1069

0.6743

 AACCTG

0.14

0.178

0.100

0.0259 *

0.142

 AACTTG

0.097

0.089

0.105

0.589

1.00

 GCTTTC

0.094

0.074

0.116

0.1598

0.8367

 AATTTC

0.01

0.015

0.005

0.3454

1.00

AHR Block 2

 GACTCAGGG

0.231

0.232

0.231

0.9865

1.00

 AGCTCAGGG

0.198

0.193

0.205

0.7632

1.00

 GATTTAAGG

0.159

0.184

0.132

0.16

0.8367

 GGCTCAGGG

0.128

0.119

0.137

0.5925

1.00

 GATCTAAGG

0.081

0.073

0.089

0.5716

1.00

 GATTCTGTA

0.069

0.059

0.079

0.4451

1.00

 GGCTCTGGG

0.066

0.054

0.079

0.3323

1.00

 GATCCAAGG

0.033

0.030

0.037

0.6932

1.00

 GATTCAGGA

0.01

0.020

0.000

0.0512

0.3157

CYP1A1

 AACT

0.656

0.649

0.663

0.7604

1.00

 ACCT

0.189

0.193

0.184

0.8228

1.00

 GCCC

0.094

0.104

0.084

0.5039

0.9829

 ACTC

0.054

0.045

0.063

0.4136

0.9422

CYP1A2

 GAT

0.64

0.614

0.668

0.2606

0.8454

 GCC

0.286

0.292

0.279

0.7736

1.00

 GAC

0.048

0.059

0.037

0.2985

0.888

 AAC

0.026

0.035

0.016

0.2365

0.8278

CYP1B1 Block 1

 TTGG

0.377

0.390

0.362

0.5704

1.00

 GTAC

0.249

0.276

0.220

0.1999

0.8872

 TTAC

0.207

0.179

0.238

0.1535

0.8046

 TCGG

0.161

0.144

0.179

0.3404

1.00

CYP1B1 Block 2

 ACTCGATT

0.268

0.277

0.258

0.6658

1.00

 CGTCGGTC

0.258

0.248

0.268

0.6364

1.00

 CGTTAGTC

0.194

0.188

0.200

0.7667

1.00

 CGCTGACC

0.186

0.163

0.210

0.2309

0.9115

 CGTCAATC

0.036

0.054

0.016

0.0392 *

0.1666

 CGTTAATC

0.015

0.015

0.016

0.9386

1.00

 CGCTAGCC

0.013

0.015

0.011

0.7029

1.00

  1. AHR Block 1 SNPs 1, 2, 3, 4, 5, 7, AHR Block 2 SNPs 8, 9, 10, 11, 12, 13, 14, 15, 16, CYP1A1 SNPs 1, 2, 3, 4, CYP1A2 SNPs 1, 2, 3, CYP1B1 Block 1 SNPs 1, 2, 3, 4, CYP1B1 Block 2 SNPs 5, 6, 7, 8, 9, 10, 11, 12
  2. *Statistically significant (P < 0.05)