Gene/SNP Genotypes CD UC IBD Controls (Reference Allele) (%) (%) (%) (%) PTPN11           Rs11066320 AA 10.6 10.4 10.5 8.2 AG 44.7 35.8 39 24.6 GG 44.7 53.8 50.5 67.2 A 32.9 28.4 30 20.5 G 67.1 71.6 70 79.5 Rs12423190 CC 0 0 0 0 CT 13.2 19.4 17.1 23.4 TT 86.8 80.6 82.9 76.6 C 6.6 9.7 8.6 12.8 T 93.4 90.3 91.4 87.2 Rs11066323 AA 10.8 2.9 5.8 2.6 AG 24.3 25.4 25 26.9 GG 64.9 70.2 69.2 70.5 A 20.3 15.9 18.3 16 G 79.7 84.1 81.7 84 TNFα           Rs1800629 AA 5.1 1.5 65.1 3.9 AG 33.3 31.3 32.1 23.2 GG 61.6 67.2 2.8 72.9 A 21.8 17.2 18.8 15.5 G 78.2 82.8 81.2 84.5 Rs361525 AA 2.7 0 0 0 AG 8.1 17.9 14.6 18.5 GG 89.2 82.1 85.4 81.5 A 6.8 9 8.2 9.3 G 93.2 91 91.8 90.7 IL23R           Rs11805303 TT 15.8 17.9 17.2 8.2 TC 42.1 40.3 40.9 46.8 CC 42.1 41.8 41.9 45 T 36.8 38.1 37.6 31.6 C 36.2 61.9 62.4 68.4 PTPN2           Rs2542151 GG 2.7 7.4 5.7 1.2 GT 16.2 13.2 14.3 21.4 TT 81.1 79.4 80 77.4 G 10.8 14 12.9 11.9 T 89.2 86 87.1 88.1 PTPN22           Rs1310182 AA 18.4 17.9 18.1 13.2 AG 42.1 41.8 41.9 43.7 GG 39.5 40.3 40 43.1 A 39.5 38.8 39 36.3 G 60.5 61.2 61 63.7 Rs2476601 AA 0 0 0 0 AG 2.7 4.5 3.9 2.5 GG 97.3 95.5 96.1 97.5 A 1.4 2.3 1.9 1.3 G 98.6 97.7 98.1 98.7 Rs2488457 CC 75 66.7 69.8 67.3 CG 19.4 30 26 30.1 GG 5.6 3.3 4.2 2.6 C 84.7 81.7 82.8 82.4 G 15.3 18.3 17.2 17.6 IL2           Rs2069763 AA 0 4.9 3.1 2.5 AC 22.2 21.3 21.6 18.5 CC 77.8 73.8 75.3 79 A 11.1 8.6 13.9 11.8 C 88.9 84.4 86.1 88.2 Rs11575812 AA 52.8 57.1 56 47.4 AG 41.7 30.2 34 43.6 GG 5.5 12.7 10 9 A 73.6 72.2 73 69.2 G 26.4 27.8 27 30.8 Rs2069762 AA 32.4 35.8 34.6 32.3 CA 54.1 41.8 46.2 45.2 CC 13.5 22.4 19.2 22.5 A 59.5 56.7 57.7 54.8 C 40.5 43.3 42.3 45.2 Rs6822844 GG 91.2 82.5 85.6 89.7 GT 0.8 17.5 14.4 10.3 TT 0 0 0 0 G 95.6 91.3 92.8 94.8 T 0.4 8.7 7.2 5.2 IL10           Rs1800872 GG 55.6 47 50 43.6 GT 41.7 45.5 44.1 51.9 TT 2.7 7.5 5.9 4.5 G 76.4 69.7 72.1 69.6 T 23.6 30.3 27.9 30.4 Rs1800871 AA 5.4 8.9 7.7 5.9 AG 37.8 49.3 45.2 48.3 GG 56.8 41.8 47.1 45.8 A 24.3 33.6 30.3 30.1 Rs1800896 G 75.7 66.4 69.7 69.9 CC 18.4 7.6 11.6 14.9 CT 36.8 48.5 44.2 47.4 TT 44.8 43.9 44.2 37.7 C 36.8 31.8 33.7 38.6 T 63.2 68.2 66.3 61.4 Rs3024498 CC 2.7 0 0.9 2 CT 25 29.2 26.2 26.5 TT 72.3 70.8 72.9 71.5 C 15.3 14.6 14 15.2 T 84.7 85.4 86 84.8 Rs3024495 CC 72.3 76.5 75 78.2 CT 25 22.1 23.1 20.5 TT 2.7 1.4 1.9 1.3 C 84.7 87.5 86.5 84.8 T 15.3 12.5 13.5 15.2

Table 3: Genotype and allele frequencies of PTPN11, TNFα, IL23R, PTPN2, PTPN22, IL2 and IL10 in patients with CD, UC, IBD and unaffected controls.