Table 2

Genetic association study results for SNPs with nominal p < 0.05.

SNP

Gene

Alleles

(Minor/Major)

MAF (Cases; Controls)

χ2 test P-value

LRT


Combined

Canadian

Belgian

P-value

FDR


rs7248389

PEPD

T/C

0.395; 0.478

0.404; 0.493

0.379; 0.469

0.0009

0.0220

0.0084

0.001

0.037

rs8891401

PEPD

C/T

0.326; 0.395

0.328; 0.411

0.320; 0.386

0.0043

0.0248

0.0513

0.0025

0.088

rs2267574

CD22

A/T

0.105; 0.147

0.106; 0.180

0.110; 0.129

0.0112

0.0047

0.4185

0.016

0.15

rs2241380

PEPD

G/A

0.419; 0.362

0.436; 0.371

0.404; 0.356

0.0184

0.0831

0.1536

0.035

0.185

rs756796

CD22

A/G

0.280; 0.230

0.273; 0.222

0.289; 0.234

0.02

0.1179

0.068

0.016

0.164

rs7250833

PEPD

T/C

0.332; 0.282

0.328; 0.278

0.337; 0.285

0.0317

0.1582

0.0987

0.043

0.219

rs7251432

HAMP

A/G

0.511; 0.459

0.520; 0.437

0.506; 0.472

0.0361

0.0296

0.5193

0.050

0.210

rs11880064

PEPD

C/T

0.415; 0.364

0.431; 0.371

0.402; 0.360

0.0367

0.1045

0.2124

0.059

0.190

rs580391

GPI

A/C

0.203; 0.243

0.196; 0.245

0.218; 0.243

0.0519

0.1143

0.4012

0.038

0.237


Tests for allelic association were carried out by a χ2 test for each SNP. P-values < 0.05 are shown in bold. The genotypic test of association was performed using the general linear mixed model approach implemented in the Statistical Analysis for Genetic Epidemiology (S.A.G.E.) [35] program ASSOC, which yields the likelihood ratio test (LRT) and the Wald statistics. Only LRT results are reported here since both LRT and Wald gave similar results. SNPs are ranked here by χ2 test p-value in the combined population. In the alleles column minor allele is listed first based on the results seen in controls. For rs7251432 the minor allele was different for cases than controls.

1SNP was out of Hardy-Weinberg equilibrium in Belgian controls.

Lillvis et al. BMC Medical Genetics 2011 12:14   doi:10.1186/1471-2350-12-14

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