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Table 5 Comparison of haplotype frequencies (additive model), as tested by chi-square analysis and permutations test, HS vs. HR samples, entire cohort (N = 211)

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

0.479

0.487

0.470

0.7288

1.00

 AATTCC

0.171

0.138

0.207

0.0613

0.5326

 AACCTG

0.133

0.165

0.096

0.0365 *

0.3665

 AACTTG

0.097

0.094

0.101

0.8016

1.0000

 GCTTTC

0.090

0.071

0.111

0.1553

0.8236

 AATTTC

0.024

0.031

0.015

0.2781

0.9680

AHR Block 2

 GACTCAGGG

0.243

0.249

0.237

0.7678

1.00

 AGCTCAGGG

0.187

0.174

0.201

0.464

1.00

 GATTTAAGG

0.152

0.175

0.126

0.17

0.8445

 GGCTCAGGG

0.119

0.108

0.132

0.4426

1.0000

 GATCTAAGG

0.075

0.066

0.085

0.4563

1.0000

 GATTCTGTA

0.071

0.058

0.086

0.267

0.9607

 GGCTCTGGG

0.061

0.049

0.075

0.2578

0.9456

 GATCCAAGG

0.033

0.031

0.035

0.8143

1.00

 GATTCAGGA

0.026

0.045

0.005

0.0109 *

0.0786

 GACTCAAGG

0.012

0.018

0.005

0.225

0.9396

CYP1A1

 AACT

0.623

0.603

0.646

0.3543

0.9613

 ACCT

0.185

0.192

0.177

0.6882

0.9998

 GCCC

0.107

0.125

0.086

0.1936

0.7935

 ACTC

0.050

0.040

0.061

0.3355

0.9493

 ACCC

0.036

0.040

0.030

0.5845

0.9975

CYP1A2

 GAT

0.602

0.562

0.646

0.0787

0.4736

 GCC

0.280

0.277

0.283

0.8902

1.00

 AAC

0.062

0.089

0.030

0.0119 *

0.1239

 GAC

0.057

0.071

0.040

0.1697

0.7649

CYP1B1 Block 1

 TTGG

0.360

0.364

0.357

0.8781

1.00

 GTAC

0.261

0.301

0.215

0.0444 *

0.2237

 TTAC

0.208

0.176

0.244

0.086

0.5013

 TCGG

0.159

0.138

0.182

0.2232

0.8763

CYP1B1 Block 2

 ACTCGATT

0.256

0.254

0.258

0.9417

1.00

 CGTCGGTC

0.251

0.237

0.268

0.4627

1.00

 CGCTGACC

0.185

0.156

0.217

0.1078

0.6369

 CGTTAGTC

0.182

0.174

0.192

0.6369

1.00

 CGTCAATC

0.037

0.057

0.015

0.0248

0.1204

 ACTTGATC

0.028

0.052

0.000

0.0011 **

0.0042 **

 CGTTAATC

0.020

0.024

0.015

0.5256

1.00

 CGCTAGCC

0.012

0.013

0.010

0.7551

1.00

 ACTCGATC

0.010

0.010

0.010

0.9756

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)
  3. **Statistically significant (P < 0.005)
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Human Genomics

ISSN: 1479-7364