. Author manuscript; available in PMC: 2009 Aug 1.

Published in final edited form as: Gastroenterology. 2008 Oct 25;136(2):523–9.e3. doi: 10.1053/j.gastro.2008.10.032

Table 3.

Loci Showing No Significant Association With Ulcerative Colitis

				UC cases		Combined controls
SNP	CHR	Gene	CD risk allete	RAF	N	RAF controls	N	P values	CD OR	Power (%)	N cases for 80% power
rs7927894	11q13	C11orf30	T	0.420	2447	0.392	4026	.0019	1.13	57	3525
rs10188217^a	2p16	PUS10	C	0.538	2406	0.507	2497	.0024	1.14	54	3634
rs1456893	7p12		A	0.698	2456	0.678	4005	.0130	1.18	85	2223
rs762421	21q22	ICOSLG	G	0.415	2434	0.393	4045	.0165	1.16	81	2373
rs1551398	8q24		A	0.630	2465	0.609	2475	.0334	1.14	51	3929
rs7758080	6q25		G	0.276	2342	0.257	2491	.0352	1.07	5	17,290
rs4807569	19p13		C	0.218	2425	0.203	4047	.0363	1.12	28	5851
rs991804	17q12	CCL2, CCL7	C	0.739	2466	0.721	2492	.0428	1.09	11	10,760
rs11175593	12q12	LRRK2, MUC19	T	0.019	2455	0.014	4060	.0541	1.49	41	4578
rs780094	2p23	GCKR	T	0.399	2464	0.382	4002	.0590	1.10	29	5891
rs2274910	1q23	ITLN2	C	0.691	2417	0.675	2472	.0790	1.17	67	2985
rs3764147	13q14		G	0.222	2424	0.210	4017	.1075	1.23	95	1664
rs1736135	21q21		T	0.588	2432	0.575	4032	.1624	1.15	74	2702
rs7749278	6q27	CCR6	T	0.519	2466	0.525	4046	.4382	1.15	76	2635
rs17309827	6p25	SLC22A23	T	0.631	2468	0.628	4045	.7070	1.07	9	12,060
rs2872507^b	17q12	ORMDL3	A	0.490	643	0.484	4050	.7175	1.15	21	1880
rs2476601	1p13	PTPN22	G	0.905	2471	0.903	2483	.7426	1.26	54	3720
rs9286879	1q24		G	0.243	2334	0.245	2490	.8002	1.15	45	4100
rs8098673	18q11		C	0.324	2467	0.325	2493	.9300	1.06	4	20,950

NOTE. UC cases include all individuals with UC whose genotyping data passed QC. P values are those from a Cochran-Armitage trend test. Power calculated assuming a multiplicative disease model, a population prevalence of 0.0024,²¹ and a false-positive rate of 0.0017. Crohn’s disease odds ratios are taken from Barrett et al (2008)¹² and represent the estimated allelic risk from the combined case/control and TDT analyses. RAF, risk increasing allele frequency.

SNP selection for the current experiment was carried out using preliminary results from Barrett et al 2008,¹² and an alternative SNP to that reported in the final analysis (rs13003464) was selected at this locus (for the purpose of calculating power, we use the OR reported for rs13003464).

Genotyping did not pass QC procedures for 1 of 2 case batches; hence, only 643 cases were available at this SNP.