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. 2012 Sep 12;28(22):2898–2904. doi: 10.1093/bioinformatics/bts553

Table 2.

The SNPs identified by EB2 model after initial filtering

SNP Gene Alleles MAF
 P-value
 OR T1D SNP r2
Control Case Fisher’s EB2
rs3184504 SH2B3 TInline graphicC 0.53 0.41 Inline graphic Inline graphic 0.62 rs3184504 1
rs72650660 CLEC16A CInline graphicT 0.043 0.011 Inline graphic Inline graphic 0.25 – –
rs8052325 CLEC16A AInline graphicG 0.13 0.082 Inline graphic Inline graphic 0.60 rs12708716 0.26
rs2476601 PTPN22 GInline graphicA 0.093 0.15 Inline graphic Inline graphic 1.72 rs2476601 1
rs3827734 PTPN22 AInline graphicT 0.0025 0.020 Inline graphic Inline graphic 8.14 – –
rs1800521 AIRE TInline graphicC 0.23 0.32 Inline graphic Inline graphic 1.58 rs760426 0.04
rs11594656 0.0029
rs28360489 IL2RA CInline graphicT 0.11 0.084 0.039 Inline graphic 0.74 rs2104286 0.10
rs12722495 0.62

OR is odds ratio of minor allele for T1D. r2 is the correlation coefficient with the most associated independent T1D SNPs (marker SNPs that have been identified associated with T1D before) in each region (http://www.t1dbase.org/page/Regions).