Table 2

Analysis of all JIA nominally associated SNP in oligoarthritis and polyarthritis subtypes in UK discovery cohort, the US validation cohort and combined meta-analysis

						UK JIA oligoarthritis and RF-negative polyarthritis cases (n=798)				US JIA oligoarthritis and RF-negative polyarthritis cases (n=813)
SNP	Chr	Position	Gene	Minor allele	Major allele	MAF cases	MAF controls	pTREND	OR (95% CI)	MAF cases	MAF controls	pTREND	OR (95% CI)	Combined meta-analysis p value	OR (95% CI)	Breslow–Day p value
rs4272626	1	116149950	NHLH2	T	C	0.34	0.36	0.07	0.90 (0.81 to 1.01)	0.36	0.37	0.33	0.95 (0.84 to 1.06)	0.05	0.92 (0.85 to 1.0)	0.55
rs11586238	1	117064661	CD2	G	C	0.26	0.24	0.10	1.11 (0.98 to 1.25)	0.22	0.24	0.39	0.94 (0.83 to 1.08)	0.56	1.03 (0.94 to 1.12)	0.08
rs1773560	1	165688387	CD247	G	A	0.39	0.42	0.008	0.86 (0.77 to 0.96)	0.38	0.41	0.01	0.87 (0.78 to 0.97)	2.8×10⁻⁴	0.86 (0.8 to 0.92)	0.93
rs10919563	1	196967065	PTPRC	A	G	0.09	0.13	4.2×10⁻⁶	0.65 (0.54 to 0.78)	0.14	0.12	0.08	1.16 (0.98 to 1.36)	0.04	0.88 (0.78 to 0.99)	3.3×10⁻⁶
rs874040	4	25717295	RBPJ	G	C	0.33	0.30	0.04	1.14 (1.01 to 1.28)	0.31	0.30	0.59	1.03 (0.92 to 1.16)	0.07	1.08 (0.99 to 1.18)	0.27
rs2736340	8	11381382	BLK	T	C	0.28	0.24	0.007	1.19 (1.05 to 1.36)	0.26	0.26	0.99	1.00 (0.88 to 1.13)	0.06	1.09 (1.0 to 1.19)	0.05
rs706778	10	6138955	IL2RA	T	C	0.45	0.40	0.002	1.20 (1.07 to 1.35	0.46	0.40	0.0002	1.24 (1.11 to 1.38)	9.5×10⁻⁷	1.22 (1.13 to 1.32)	0.74
rs2872507	17	35294289	ORMDL3	A	G	0.53	0.48	0.001	1.22 (1.08 to 1.37)	0.46	0.46	0.93	0.99 (0.89 to 1.11)	0.03	1.09 (1.01 to 1.18)	0.01
rs7234029	18	12867060	PTPN2	G	A	0.20	0.16	9.3×10⁻⁶	1.35 (1.18 to 1.54)	0.23	0.16	1.3×10⁻⁸	1.48 (1.29 to 1.69)	8.1×10⁻¹³	1.41 (1.28 to 1.55)	0.33

Breslow–Day p value is a measure of whether there is significant difference in the OR in the two cohorts.
Chr, chromosome; JIA, juvenile idiopathic arthritis; MAF, minor allele frequency; pTREND, p value for the Armitage test for trend as generated in PLINK; SNP, single-nucleotide polymorphism.