Table 5. Allele Frequency of Highly Significant IBD Associated SNPs in Crohn's Disease with Colonic Involvement and Healthy Controls.

Chr	SNP	Gene	Assoc IBD Subtype	Freq in L2 CD n = 228	Freq in Healthy Controls = 1057	OR	P-value
1	rs2476601	PTPN22	CD	0.0540	0.0863	0.606	0.025
1	rs11465804	IL23R	CD and UC	0.0181	0.0567	0.309	0.001
1	rs10889677	IL23R	UC	0.4077	0.3282	1.387	0.002
3	rs3197999	MST1	CD and UC	0.3439	0.2870	1.230	0.018
3	rs9858542	MST1	UC	0.3484	0.2939	1.283	0.024
6	rs2395185	HLA-DRA	UC	0.2658	0.3255	0.744	0.013
5	rs11747270	IRGM	CD	0.1674	0.0978	1.837	<0.001
7	rs1456893	?	CD	0.2455	0.3100	0.721	0.007
10	rs17582416	CCNY	CD	0.4099	0.3416	1.330	0.007
10	rs10995271	ZNF365	CD	0.4638	0.3976	1.313	0.010
11	rs7927894	C11orf30	CD	0.4568	0.3942	1.287	0.016
16	rs2066845	NOD2	CD	0.0383	0.0172	2.334	0.005
18	rs2542151	PTPN2	CD	0.2014	0.1553	1.388	0.016
21	rs2836878	PSMG1	CD and UC	0.2185	0.2715	0.753	0.022

Chr = chromosome, SNP = single nucleotide polymorphism, CD = Crohn's disease, UC = ulcerative colitis, IBDU = inflammatory bowel disease-unclassified, L2 = colon-only CD location, Freq = minor allele frequency, OR = odds ratio.