Table 1.

Genome-wide significant associations in oligoarticular and RF-negative polyarticular JIA.

Locus	Chr	SNP	Best p value	MAF control	MAF case	OR	SNP position
PTPN22*	1	rs6679677	3.2 × 10−25	0.10	0.14	1.59	Intergenic
ATP8B2-IL6R	1	rs11265608	2.8 10−8	0.10	0.12	1.33	Intergenic
STAT4	2	rs10174238	1.3 × 10−13	0.23	0.28	1.29	Intron
IL2-IL21	4	rs1479924	6.2 × 10−11	0.29	0.24	0.79	Intergenic
ANKRD55	5	rs71624119	4.4 × 10−11	0.25	0.20	0.78	Intron
ERAP2-LNPEP	5	rs27290	7.5 × 10−9	0.44	0.47	1.32	Intron
C5orf56-IRF1	5	rs4705862	1.0 × 10−8	0.44	0.39	0.84	Intergenic
HLA DQB1-DQA2*	6	rs7775055	3.1 × 10−174	0.02	0.12	6.01	Intergenic
IL2RA	10	rs7909519	8.0 × 10−10	0.11	0.08	0.72	Intron
FAS	10	rs7069750	2.9 × 10−8	0.44	0.48	1.18	Intron
SH2B3-ATXN2	12	rs3184504	2.6 × 10−9	0.49	0.54	1.20	Coding
ZFP36L1	14	rs12434551	1.6 × 10−8	0.47	0.43	0.77	Intergenic
PTPN2*	18	rs2847293	1.4 × 10−12	0.17	0.20	1.31	Intergenic
TYK2	19	rs34536443	1.0 × 10−10	0.05	0.03	0.56	Coding
RUNX1	21	rs9979383	1.1 × 10−8	0.37	0.33	0.78	Intergenic
UBE2L3	22	rs2266959	6.2 × 10−9	0.19	0.22	1.24	Intron
IL2RB	22	rs2284033	1.6 × 10−8	0.44	0.39	0.84	Intron

Chr: chromosome; SNP: Single nucleotide polymorphism; MAF: Minor allele frequency; OR: Odds ratio.

^*indicates associations that had been described previously at genome wide levels of significance.

From Hinks A, Cobb J, Marion MC, Prahalad S, Sudman M, Bowes J, et al. Dense genotyping of immune-related disease regions identifies 14 new susceptibility loci for juvenile idiopathic arthritis. Nat Genet 2013; 45:664–9.