Table 1 ∣.

Novel RA risk loci detected in this study

									Allele freq. in 1KG Phase 3
rs ID	Chr.	Position	Nearest gene	Predicted causal gene	OR	L95	U95	P value	EAS	EUR	AFR	SAS
rs41269479	1	42,166,782	HIVEP3	NA	1.15	1.09	1.20	2.51 × 10−8	0.26	0.28	0.08	0.42
rs41313373	1	92,940,411	GFI1	GFI1 (eQTL)	1.12	1.08	1.16	1.08 × 10−8	0.01	0.14	0.01	0.10
rs1188620266	1	235,800,357	GNG4	NA	0.91	0.88	0.94	2.06 × 10−8	0.83	0.61	0.22	0.70
rs143259280	2	70,209,168	PCBP1-AS1	C2orf42 (eQTL)	1.09	1.06	1.12	2.13 × 10−8	0.46	0.32	0.89	0.32
rs77574423	3	11,984,744	TAMM41, SYN2	SYN2 (eQTL)	1.10	1.07	1.14	1.35 × 10−8	0.56	0.72	0.57	0.74
rs62264113	3	127,292,333	TPRA1	NA	0.92	0.89	0.95	4.66 × 10−8	0.27	0.08	0.01	0.21
rs4687070	3	189,306,650	TPRG1, TP63	NA	1.15	1.09	1.20	6.07 × 10−9	0.02	0.07	0.03	0.14
rs4690029	4	2,722,815	FAM193A	TNIP2 (p.A313V)	0.94	0.92	0.96	2.83 × 10−9	0.40	0.41	0.59	0.47
rs138066321	4	80,952,409	ANTXR2	ANTXR2 (eQTL)	0.93	0.91	0.95	4.48 × 10−10	0.38	0.45	0.09	0.32
rs58107865	4	109,061,618	LEF1	NA	0.84	0.80	0.88	4.92 × 10−14	0.21	0.01	0.00	0.03
rs56787183	5	40,499,290	LINC00603, PTGER4	NA	0.85	0.80	0.90	2.15 × 10−9	0.09	0.00	0.04	0.02
rs244468	5	142,604,421	ARHGAP26	NA	1.07	1.05	1.10	8.19 × 10−9	0.79	0.51	0.41	0.60
rs1422673	5	150,438,988	TNIP1	NA	1.10	1.06	1.14	1.56 × 10−8	0.50	0.19	0.39	0.29
rs113532504	6	15,195,682	LINC01108, JARID2	JARID2 (eQTL)	1.10	1.07	1.14	3.42 × 10−8	0.06	0.10	0.36	0.10
rs67318457	6	23,925,021	LOC105374972, NRSN1	NA	1.08	1.05	1.11	1.10 × 10−8	0.14	0.27	0.37	0.05
rs940825	7	17,207,164	AGR3, AHR	NA	1.11	1.07	1.16	3.39 × 10−8	0.18	0.12	0.05	0.06
rs182199544	7	27,084,581	SKAP2, HOXA1	HOXA5 (eQTL)	0.87	0.84	0.91	3.61 × 10−9	0.01	0.08	0.36	0.03
rs6583441	7	50,361,874	IKZF1	NA	0.95	0.93	0.97	4.69 × 10−8	0.53	0.47	0.33	0.41
rs6979218	7	99,893,148	CASTOR3, SPDYE3	PILRA (p.R78G) PVRIG (p.N81D)	1.09	1.06	1.12	2.24 × 10−11	0.38	0.75	0.91	0.72
rs11777380	8	134,211,965	WISP1	NA	0.92	0.90	0.95	3.00 × 10−10	0.17	0.32	0.08	0.19
rs911760	9	5,438,435	PLGRKT	NA	1.15	1.09	1.20	2.15 × 10−8	0.23	0.19	0.33	0.28
rs734094	11	2,323,220	C11orf21, TSPAN32	NA	1.08	1.05	1.10	3.40 × 10−8	0.19	0.40	0.43	0.45
rs1427749	12	46,370,116	SCAF11	ARID2 (eQTL)	0.93	0.90	0.95	1.17 × 10−8	0.89	0.80	0.91	0.95
rs61944750	13	28,634,933	FLT3	NA	0.91	0.88	0.94	1.69 × 10−8	0.05	0.21	0.09	0.09
rs2147161	13	42,982,302	AKAP11, LINC02341	NA	1.10	1.06	1.13	2.73 × 10−8	0.13	0.21	0.02	0.28
rs175714	14	75,981,856	JDP2, BATF	NA	0.94	0.92	0.96	4.14 × 10−8	0.43	0.60	0.30	0.64
rs115284761	15	77,326,836	PSTPIP1	NA	0.91	0.89	0.94	1.71 × 10−11	0.28	0.25	0.15	0.23
rs11375064	17	25,904,074	KSR1	KSR1 (eQTL)	1.08	1.05	1.11	3.92 × 10−8	0.44	0.60	0.53	0.47
rs591549	18	3,542,247	DLGAP1	NA	0.91	0.88	0.94	9.14 × 10−9	0.35	0.68	0.42	0.61
rs371734407	18	60,009,634	TNFRSF11A	NA	1.10	1.06	1.14	4.14 × 10−8	0.44	0.59	0.50	0.52
rs10415976	19	941,603	ARID3A	NA	0.92	0.90	0.95	2.90 × 10−8	0.47	0.08	0.35	0.25
rs55762233	19	19,367,319	HAPLN4	CILP2 (eQTL), HAPLN4 (eQTL), SUGP1 (eQTL), TM6SF2 (eQTL), TSSK6 (eQTL), YJEFN3 (eQTL)	1.10	1.07	1.14	1.43 × 10−9	0.02	0.17	0.32	0.14
rs28373672	19	36,213,072	KMT2B	IGFLR1 (eQTL), LIN37 (eQTL)	0.93	0.91	0.96	3.33 × 10−8	0.24	0.23	0.62	0.29
rs8106598	19	52,017,940	SIGLEC12, SIGLEC6	NA	1.08	1.05	1.11	3.12 × 10−8	0.08	0.22	0.32	0.17

Statistics in the GWAS setting with the lowest P values are provided (see Supplementary Table 4 for details). GWAS statistics were calculated by a fixed effect meta-analysis of results from logistic regression tests in each cohort. The genomic coordinate is according to GRCh37. rs ID, reference single nucleotide polymorphism cluster identification number; Chr., chromosome; Predicted causal gene, predicted molecular consequences using eQTLs or non-synonymous variants (see Supplementary Tables 8-10 for details); NA, not applicable; OR, odds ratio (the effect allele is the alternative allele); L95, lower 95% confidence interval; U95, upper 95% confidence interval; Allele freq., allele frequency of the effect allele.