Table 2

Non-HLA SNPs associated with p value <5E-05 in the combined analysis of The Netherlands I, The Netherlands II and Spain populations

			Spain			The Netherlands I			The Netherlands II			Combined
Chr position (bp)	SNP	Locus	P	OR (CI)	MAF ACPA−/CTRL	P	OR (CI)	MAF ACPA−/CTRL	P	OR (CI)	MAF ACPA−/CTRL	P_invVar	OR	Q
1 (58 814 769)	rs14008	TACSTD2*	1.43E-02	0.43 (0.22–0.85)	0.02/0.05	1.90E-05	0.50 (0.36–0.69)	0.04/0.07	0.95	0.98 (0.53–1.83)	0.05/0.05	7.40E-06	0.55	0.12
1 (81 205 529)	rs6684037	LPHN2	0.10	0.66 (0.40–1.09)	0.04/0.06	1.17E-04	0.51 (0.36–0.72)	0.03/0.07	0.41	0.72 (0.34–1.55)	0.03/0.04	3.70E-05	0.57	0.56
1 (151 350 870)	rs383582	SPRR2F	0.49	1.13 (0.80–1.60)	0.11/0.09	6.00E-06	1.63 (1.32–2.01)	0.13/0.09	0.40	1.19 (0.79–1.79)	0.11/0.10	2.52E-05	1.42	0.14
2 (234 061 305)	rs10929178	USP40	0.20	1.24 (0.89–1.71)	0.13/0.10	5.62E-05	1.51 (1.24–1.84)	0.14/0.10	0.46	1.17 (0.78–1.74)	0.11/0.10	4.80E-05	1.39	0.39
3 (55 865 516)	rs7609626	ERC2	4.22E-04	0.44 (0.28–0.70)	0.04/0.10	1.05E-03	0.60 (0.45–0.82)	0.05/0.08	0.30	0.68 (0.33–1.39)	0.04/0.05	1.91E-06	0.56	0.45
3 (64 112 733)	rs929701	PRICKLE2	0.11	1.34 (0.93–1.93)	0.11/0.09	7.71E-04	1.43 (1.16–1.76)	0.13/0.10	0.06	1.44 (0.99–2.11)	0.14/0.11	3.23E-05	1.42	0.95
3 (65 270 367)	rs13100540	ADAMTS9-AS2—MAGI1	0.23	1.15 (0.91–1.45)	0.33/0.30	6.70E-05	1.33 (1.15–1.52)	0.38/0.33	0.19	1.20 (0.92–1.57)	0.39/0.35	2.41E-05	1.26	0.54
3 (106 853 033)	rs9857831	ALCAM—CBLB	1.10E-02	1.36 (1.07–1.72)	0.36/0.31	1.64E-02	1.19 (1.03–1.36)	0.37/0.33	1.07E-02	1.42 (1.08–1.85)	0.42/0.34	3.94E-05	1.26	0.40
4 (102 253 020)	rs2732512	PPP3CA	0.12	1.42 (0.91–2.23)	0.07/0.05	1.26E-02	1.47 (1.09–2.00)	0.05/0.04	1.72E-03	2.09 (1.32–3.31)	0.09/0.05	4.67E-05	1.58	0.40
5 (126 163 281)	rs17598783	LMNB1*	0.29	1.13 (0.90–1.42)	0.33/0.31	1.89E-03	1.24 (1.08–1.43)	0.36/0.32	2.61E-03	1.50 (1.15–1.96)	0.42/0.32	3.32E-05	1.26	0.27
5 (165 080 723)	rs12657428	TENM2	9.32E-04	2.49 (1.45–4.27)	0.06/0.03	7.16E-04	1.77 (1.27–2.45)	0.05/0.03	0.92	1.03 (0.57–1.86)	0.05/0.05	2.61E-05	1.72	0.09
7 (9 537 527)	rs6463923	NXPH1*	0.13	0.84 (0.68–1.05)	0.35/0.36	1.36E-06	0.71 (0.62–0.82)	0.33/0.41	0.35	0.88 (0.67–1.16)	0.36/0.39	1.14E-06	0.77	0.25
7 (19 498 740)	rs10216141	TWISTNB	5.34E-03	2.29 (1.28–4.11)	0.05/0.02	3.57E-02	1.48 (1.03–2.13)	0.04/0.02	1.13E-02	2.06 (1.18–3.60)	0.06/0.03	4.53E-05	1.76	0.38
7 (108 372 672)	rs848324	THAP5	3.67E-03	0.44 (0.25–0.77)	0.03/0.07	5.25E-04	0.55 (0.39–0.77)	0.04/0.06	0.99	0.99 (0.52–1.89)	0.04/0.04	4.29E-05	0.58	0.16
7 (140 342 281)	rs38723	BRAF-MRPS33*	2.78E-03	0.42 (0.24–0.74)	0.03/0.06	2.70E-05	0.48 (0.34–0.68)	0.03/0.07	0.22	0.64 (0.31–1.31)	0.03/0.05	1.77E-07	0.49	0.67
7 (140 426 209)	rs557962	Transmembrane protein 178-like	1.14E-04	0.40 (0.25–0.64)	0.04/0.09	2.19E-03	0.66 (0.50–0.86)	0.06/0.09	0.50	0.83 (0.49–1.42)	0.06/0.07	7.87E-06	0.61	0.09
8 (18 286 035)	rs17642674	NAT1—NAT2	0.07	1.35 (0.98–1.86)	0.14/0.10	3.61E-03	1.35 (1.10–1.65)	0.13/0.10	1.16E-02	1.59 (1.11–2.27)	0.16/0.11	2.90E-05	1.39	0.72
9 (120 110 400)	rs7047525	TLR4*	3.25E-02	0.72 (0.54–0.97)	0.15/0.18	1.99E-04	0.67 (0.54–0.83)	0.10/0.15	0.12	0.68 (0.42–1.11)	0.08/0.12	5.70E-06	0.69	0.92
10 (69 579 808)	rs10997948	MYPN*	3.75E-02	1.57 (1.03–2.40)	0.08/0.05	3.46E-05	1.64 (1.30–2.07)	0.10/0.07	0.10	1.41 (0.93–2.14)	0.11/0.08	1.07E-06	1.58	0.83
10 (72 178 560)	rs7921298	ADAMTS14	2.98E-02	0.52 (0.29–0.94)	0.03/0.05	5.21E-04	0.55 (0.40–0.77)	0.04/0.06	0.13	0.50 (0.21–1.24)	0.02/0.04	1.35E-05	0.54	0.97
10 (84 025 408)	rs4329625	NRG3	8.90E-04	2.58 (1.48–4.52)	0.06/0.03	3.88E-04	1.96 (1.35–2.84)	0.04/0.02	0.11	1.63 (0.89–3.00)	0.05/0.03	6.10E-07	2.02	0.54
11 (60 123 089)	rs7927817	MS4A13—MR_026 946.1	0.10	1.36 (0.95–1.95)	0.11/0.09	1.39E-05	1.52 (1.26–1.83)	0.16/0.11	0.96	0.99 (0.68–1.45)	0.13/0.13	2.48E-05	1.39	0.14
11 (63,641,881)	rs3824854	FLRT1	4.71E-02	1.29 (1.00–1.66)	0.26/0.22	4.62E-03	1.29 (1.08–1.53)	0.19/0.16	2.10E-02	1.46 (1.06–2.02)	0.21/0.15	4.18E-05	1.32	0.78
11 (88,307,788)	rs518167	GRM5	9.12E-03	2.55 (1.26–5.14)	0.04/0.02	5.66E-04	2.22 (1.41–3.49)	0.03/0.01	0.21	1.66 (0.75–3.66)	0.03/0.02	9.68E-06	2.17	0.72
12 (78,361,110)	rs7959721	SYT1	0.97	1.01 (0.48–2.13)	0.02/0.02	1.53E-06	2.55 (1.74–3.74)	0.04/0.02	0.39	1.34 (0.68–2.65)	0.04/0.03	2.50E-05	1.92	0.05
13 (50 474 171)	rs3790022	RNASEH2B-FAM124A	1.19E-03	0.51 (0.34–0.77)	0.06/0.10	4.60E-04	0.62 (0.48–0.81)	0.06/0.08	0.08	0.53 (0.26–1.08)	0.03/0.06	5.56E-07	0.58	0.69
13 (99 319 102)	rs9557321	CLYBL	0.08	1.62 (0.94–2.77)	0.05/0.04	4.33E-07	2.08 (1.57–2.77)	0.07/0.04	0.07	1.48 (0.97–2.28)	0.11/0.08	4.51E-08	1.83	0.38
16 (60 319 776)	rs16963882	CDH8	4.36E-02	0.71 (0.51–0.99)	0.10/0.14	9.02E-05	0.67 (0.55–0.82)	0.12/0.16	0.80	0.95 (0.64–1.41)	0.13/0.14	3.62E-05	0.72	0.30
17 (23 876 812)	rs598858	FOXN1	0.22	1.42 (0.81–2.50)	0.05/0.03	2.45E-05	1.85 (1.39–2.47)	0.07/0.04	0.10	1.49 (0.93–2.37)	0.08/0.06	4.50E-06	1.69	0.59
17 (43 952 192)	rs11651168	SKAP1—HOXB1*	3.07E-02	0.79 (0.64–0.98)	0.44/0.50	5.45E-04	0.79 (0.69–0.90)	0.45/0.51	0.14	0.82 (0.63–1.07)	0.42/0.48	1.46E-05	0.80	0.98
18 (71 591 842)	rs1943199	SMIM21*	2.01E-03	2.84 (1.47–5.51)	0.05/0.02	1.54E-07	2.66 (1.85–3.84)	0.05/0.02	0.12	1.53 (0.90–2.61)	0.07/0.05	1.73E-09	2.33	0.20
19 (57 624 232)	rs8182486	ZNF534	2.52E-02	1.58 (1.06–2.36)	0.10/0.06	3.44E-04	1.62 (1.25–2.12)	0.07/0.05	0.45	1.20 (0.75–1.91)	0.08/0.07	3.49E-05	1.53	0.53
20 (51 981 774)	rs6013838	BCAS1	0.09	0.55 (0.27–1.11)	0.02/0.04	7.71E-05	0.40 (0.26–0.63)	0.02/0.04	0.51	0.68 (0.21–2.17)	0.01/0.02	2.33E-05	0.46	0.61
22 (21 946 433)	rs12166802	BCR (Breakpoint Cluster Region)	5.48E-03	2.18 (1.26–3.78)	0.06/0.03	2.60E-03	1.62 (1.18–2.22)	0.05/0.04	0.30	1.39 (0.74–2.60)	0.05/0.03	4.66E-05	1.68	0.53

Controls are used as reference for all comparisons.
The genome-wide significant p value is shown in bold.
CTRL, control; MAF, minor allele frequency; OR, OR for the minor allele; p, logistic regression p value including 10 PC as covariates; P_InvVar, inverse variance fixed effects combined-analysis p value; Q, Cochran Q test p value.
*Multiple signals fulfilling the selection criteria in the locus, the reported variant corresponds with the most strongly associated polymorphism.