Table 1.

Comparison of different approaches on the four SNPs identified in Nejentsev et al.’s article of which the first two SNPs within IFIH1 gene were replicated in their follow-up genotyping experiment

SNP	Location	Chr.	Alleles	P-value
				Nejentsev’s Fisher’s	Our Fisher’s	Our EB1	Our EB2
rs35337543	IFIH1, intron 8	chr2	GC	0.000044	0.0032	0.0029	0.016
rs35667974	IFIH1, exon 14	chr2	AG	0.0049	0.076	0.017	0.011
ss107794688	CLEC16A, intron 23	chr16	CT	0.016	0.045	0.0047	0.034
ss107794687	CLEC16A, intron 11	chr16	CT	0.023	0.000046	0.00021	0.000005

Since different alignment software and filters were used, our Fisher’s exact results were slightly different from Nejentsev et al.rsquo;s. Overall, all the four SNPs still showed significance in our preferred EB2 model ().