Table 4

Association results

SNP

Gene

<a onClick="popup('http://www.biomedcentral.com/1471-2164/14/S1/S1/mathml/M41','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/14/S1/S1/mathml/M41">View MathML</a>

n0

<a onClick="popup('http://www.biomedcentral.com/1471-2164/14/S1/S1/mathml/M42','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/14/S1/S1/mathml/M42">View MathML</a>

n1

Fisher's p-value

EM p-value


rs3184504

SH2B3

0.52

499

0.41

394

1.9e-6

8.4e-7

rs7076103

IL2RA

0.19

178

0.10

93

4.5e-8

2.7e-7

rs2476601

PTPN22

0.09

86

0.16

151

8.1e-6

9.2e-6


Testing for association between common SNPs <a onClick="popup('http://www.biomedcentral.com/1471-2164/14/S1/S1/mathml/M43','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/14/S1/S1/mathml/M43">View MathML</a> and T1D with Fisher's preliminary p-value at most e-5. In the table, <a onClick="popup('http://www.biomedcentral.com/1471-2164/14/S1/S1/mathml/M44','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/14/S1/S1/mathml/M44">View MathML</a> and <a onClick="popup('http://www.biomedcentral.com/1471-2164/14/S1/S1/mathml/M45','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/14/S1/S1/mathml/M45">View MathML</a> are the estimated minor allele frequencies using the EM algorithm in the controls and cases, respectively, and <a onClick="popup('http://www.biomedcentral.com/1471-2164/14/S1/S1/mathml/M46','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/14/S1/S1/mathml/M46">View MathML</a>, i = 0, 1. The Fisher's p-value is the preliminary p-value using the Fisher's exact test as in [8] and the EM p-value is the p-value calculated based on the likelihood ratio statistic in equation 8.

Chen and Sun BMC Genomics 2013 14(Suppl 1):S1   doi:10.1186/1471-2164-14-S1-S1

Open Data