Table 1. Identification of rare variants associated with ulcerative colitis.

	Follow-up genotyping			IIBDGC Immunochip data			Combined
Gene, mutation	alleles tested,			alleles tested,			alleles tested
chromosome: positiona	allele frequencyc			allele frequencyc
	UC	HC	P	UC	HC	P	UC	HC	OR (95% CI)	P
RNF186, p.Ala64Thr	14580	16034	8.69E-04	NA	NA	NA	14580	16034	1.49	8.69E-04
1: 20013992	1.21%	0.69%							(1.17–1.90)
IL23R, p.Gly149Argb	14472	15936	0.097	14262	24346	0.197	28734	40282	0.74	0.032
1: 67421184	0.25%	0.35%		0.34%	0.44%				(0.56–0.97)
IL23R, p.Val362Ileb	14566	16026	0.025	11182	21102	0.024	25748	37128	0.79	1.18E-03
1: 67478488	1.27%	1.52%		1.17%	1.48%				(0.68–0.91)
CEP72, p.Lys314Arg	10278	10534	0.012	NA	NA	NA	10278	10534	0.17	0.012
5: 690668	0%	0.095%							(0.036–0.79)
CEP72, p.Asp316Asn	14558	16034	0.043	NA	NA	NA	14558	16034	0.34	0.043
5: 690673	0.021%	0.075%							(0.12–1.00)
CCR6, p.Ala369Val	13378	14454	4.52E-04	11180	21098	0.71	24560	35552	1.26	0.013
6: 167470814	0.99%	0.66%		0.84%	0.82%				(1.05–1.51)
LAMB1, p.Ile1547Thr	13374	14450	0.018	11170	21090	0.159	27432	35540	1.16	0.017
7: 107357198	2.03%	1.61%		2.39%	2.10%				(1.03–1.30)
JAK2, p.Arg1063His	14528	15976	0.015	NA	NA	NA	14528	15976	0.65	0.015
9: 5116343	0.34%	0.58%							(0.45–0.92)
CARD9, c.IVS11+1G>Cb	7002	7146	1.21E-06	14286	24362	1.81E-06	21290	31508	0.39	1.47E-11
9: 138379413	0.31%	0.99%		0.28%	0.71%				(0.30–0.53)
STAC2, p.Lys302Arg	14580	16036	0.038	NA	NA	NA	14580	16036	1.39	0.038
17: 34624048	0.62%	0.47%							(1.02–1.90)

^aPositions from Human genome build 36.

^bPreviously reported variant independently identified in the current study.

^cMinor allele frequencies estimates from combined case:control cohorts; actual allele frequencies can vary between cohorts.

UC, Ulcerative Colitis; HC, Healthy Controls; NA, data not available.