Table 3.

Loci selected for replication from the ImmunoChip study^a

Chr.	SNP ID	Gene	Fine mappedb	Selectedc	Droppedd	Reason dropped	Minor allele	Major allele	Frequency in controlse	Frequency in anti‐CCP–negative RAe	OR	P
5	rs71624119	ANKRD55	Densely genotyped	IC/UK	No	–	A	G	0.25	0.20	IC: 0.79 UK: 0.77	IC: 6.23 × 10−12 UK: 1.20 × 10−5
5	rs528092	C5orf30	Densely genotyped	IC	No	–	C	T	0.33	0.30	0.87	1.09 × 10−5
2	rs888427	CYBRD1	Outside	IC	No	–	T	C	0.35	0.39	1.13	3.63 × 10−5
9	rs7857530	TXNDC4	Outside	IC	Yes	Incompatibility for multiplex	G	A	0.44	0.41	0.89	5.43 × 10−5
18	rs16955629	RAB31	Outside	IC	No	–	A	G	0.24	0.27	1.14	6.00 × 10−5
3	rs1875463	SLC9A9	Outside	IC	Yes	Primer design failed	T	C	0.24	0.21	0.87	7.09 × 10−5
16	rs28698667	IL27	Densely genotyped	IC	No	–	T	C	0.42	0.46	1.13	7.57 × 10−5
6	rs10440835	PRL	Outside	IC	No	–	T	C	0.33	0.36	1.12	8.00 × 10−5
7	rs16879645	ELMO1	Densely genotyped	IC	Yes	Incompatibility for multiplex	C	T	0.10	0.12	1.19	8.13 × 10−5
8	rs4840565	BLK	Densely genotyped	IC	No	–	C	G	0.27	0.31	1.13	8.53 × 10−5
6	rs9483788	HBS1L	Outside	IC	Yes	Failed to genotype	C	T	0.26	0.29	1.13	8.73 × 10−5
2	rs10181656	STAT4	Densely genotyped	IC	No	–	G	C	0.22	0.24	1.14	9.84 × 10−5
21	rs9979383	RUNX1	Outside	IC	No	–	C	T	0.37	0.33	0.89	9.90 × 10−5
16	rs79349411	IRF8	Densely genotyped	UK	Yes	Primer design failed	A	C	0.09	0.12	1.35	3.68 × 10−5
11	rs613587	FLI1	Outside	UK	No	–	G	A	0.28	0.33	1.23	5.26 × 10−5
22	rs117794103	MTMR3	Densely genotyped	UK	Yes	Failed at post‐genotyping QC	G	A	0.01	0.03	1.90	5.86 × 10−5
1	rs67087057	DPH5	Densely genotyped	UK	Yes	Failed at post‐imputation QC	T	A	0.33	0.37	1.22	6.13 × 10−5
6	rs1002475	REV3L	Densely genotyped	UK	Yes	Incompatibility for multiplex	T	C	0.44	0.49	1.20	1.20 × 10−4
1	rs10489912	NFIA	Outside	UK	No	–	A	C	0.42	0.38	0.83	1.65 × 10−4
1	rs2249707	SLAMF9	Outside	UK	No	–	C	T	0.32	0.28	0.82	1.68 × 10−4
17	rs2689	HNF1B	Outside	UK	No	–	A	T	0.48	0.44	0.84	1.75 × 10−4
2	rs116752433	KIAA1841	Densely genotyped	UK	Yes	Primer design failed	A	G	0.03	0.01	0.45	1.91 × 10−4
4	rs6533712	CAMK2D	Outside	UK	No	–	T	A	0.46	0.51	1.19	2.01 × 10−4
16	rs116899727	CLEC16A	Densely genotyped	UK	Yes	Failed to genotype	T	G	0.02	0.01	0.42	2.18 × 10−4
15	rs1444291	AGBL1	Outside	UK	Yes	Incompatibility for multiplex	C	T	0.27	0.23	0.81	2.41 × 10−4
8	rs4736558	KCNQ3	Outside	UK	Yes	MAF difference in controls	T	A	0.24	0.27	1.22	3.00 × 10−4

^aChr. = chromosome; OR = odds ratio; QC = quality control.

^bIndicates whether the single‐nucleotide polymorphism (SNP) maps to one of the 186 densely mapped regions on the ImmunoChip (IC).

^cIC indicates that the SNP was selected based on the P value of the meta‐analysis across the 6 cohorts of the IC, while UK refers to the list of SNPs from the UK ImmunoChip cohort.

^d“Dropped” indicates SNPs not available for analysis.

^eMinor allele frequency (MAF) in controls or patients with anti–cyclic citrullinated peptide (anti‐CCP)–negative rheumatoid arthritis (RA) in the UK samples from the ImmunoChip study.