Table 4. Allele Frequencies of Variants in Genes Involved in the Orchestration of the Secondary Immune Response in UC/IBDU and CD.

Chr	Gene	Assoc IBD Subtype	SNP	Freq in CD n = 1144	Freq in UC/IBDU n = 1230	Freq in HC n = 1057	P-value UC/IBDU vs. CD	P-value CD vs. HC	P-value UC/IBDU vs. HC
1p13	PTPN22	CD	rs2476601	0.0628	0.0799	0.0864	P = 0.0372	P = 0.0051	P = 0.4513
3p21	MST1	CD and UC	rs3197999	0.3348	0.3353	0.2876	P = 0.6164	P = 0.0001	P = 0.0007
3p21	MST1	UC	rs9858542	0.341	0.3426	0.2939	P = 0.8049	P = 0.0004	P = 0.0009
6p21.32	HLA-DRA	UC	rs2395185	0.3530	0.2384	0.3255	P = 3.27E-15	P = 0.1617	P = 1.85E-10
9q32	TNFSF15	CD	rs6478108	0.2980	0.2781	0.3161	P = 0.1428	P = 0.2020	P = 0.0065
9q32	TNFSF15	CD	rs4263839	0.2883	0.2650	0.3016	P = 0.0628	P = 0.3346	P = 0.0051
10p11	CCNY	CD	rs17582416	0.3936	0.3746	0.3416	P = 0.193	P = 0.0004	P = 0.0255
10q24	NKX23	CD and UC	rs11190140	0.4590	0.4641	0.5057	P = 0.7952	P = 0.0023	P = 0.0051
18p11	PTPN2	CD	rs2542151	0.1777	0.1682	0.1553	P = 0.4016	P = 0.0541	P = 0.2685
20q13.3	TNFRSF6B	CD and UC	rs2315008	0.2774	0.2777	0.3012	P = 0.6385	P = 0.2190	P = 0.0902

Chr = chromosome band, CD = Crohn's disease, UC = ulcerative colitis, IBDU = inflammatory bowel disease - unclassified, HC = healthy controls, SNP = single nucleotide polymorphism, Freq = minor allele frequency.

SNPs in bold font, significantly different (P < 0.05) frequencies between CD and UC.