Table 2: Loci Identified by Trans-Disease Meta-Analysis (TDMA).

Susie # indicates the number of pairs of fine-mapped signals with evidence of colocalization (PP>0.7)

Shared (same direction of effect) loci:
Cyt. Band	rsID	Position (hg19)	RA/NR	MS		Psoriasis		TDMA		Heterogeneity		Colocalization		Nearby Genes
				OR	P	OR	P	OR	P	Q	P	COLOC PP	SuSiE #
5q33.3	rs2546890	158759900	A/G	1.12	1.0×10−12	1.33	6.4×10−51	1.21	7.1×10−58	1.4×10−2	0.91	4.4×10−7	0	IL12B
6p21.1	rs59024520	42238973	C/T	1.16	6.3×10−5	1.19	8.2×10−5	1.17	2.3×10−8	4.4×10−4	0.98	0.83	0	USP49
6q23.3	rs9321623	137958265	C/T	1.08	4.5×10−6	1.10	4.5×10−7	1.09	9.5×10−12	1.7×10−4	0.99	1.5×10−3	1	TNFAIP3
7p14.1	rs11767350	37385365	A/G	1.07	6.5×10−6	1.09	7.4×10−6	1.08	2.2×10−10	6.4×10−5	0.99	0.80	3	ELMO1 *
10q22.2	rs2459446	75601596	C/T	1.07	7.9×10−5	1.13	1.5×10−10	1.09	8.9×10−14	1.8×10−3	0.97	0.87	3	CAMK2G *
11q13.1	rs479777	64107477	T/C	1.08	3.5×10−5	1.13	2.1×10−9	1.10	6.0×10−13	9.1×10−4	0.98	0.87	0	PRDX5 * , RPS6KA4 *
12p13.31	rs4149576	6449115	T/C	1.11	3.5×10−9	0.07	8.8×10−5	1.09	6.8×10−12	3.4×10−4	0.99	0.07	6	CD27, TNFRSF1A *
13q14.2	rs9591325	50811220	T/C	1.24	4.2×10−10	1.24	6.6×10−9	1.24	2.0×10−17	1.7×10−5	1.00	0.99	2	DLEU1 *
16p13.13	rs243324	11354970	A/G	1.12	5.9×10−12	1.08	6.6×10−5	1.10	5.5×10−15	6.6×10−4	0.98	3.1×10−4	0	SOCS1, RMI2 *
17q21.2	rs957970	40519890	A/G	1.14	1.1×10−13	1.11	7.3×10−8	1.13	6.4×10−20	2.2×10−4	0.99	0.97	7	STAT3 * , STAT5A * /B
19p13.2	rs55677033	11166293	T/C	1.09	2.6×10−6	1.08	9.0×10−5	1.09	9.5×10−10	1.0×10−5	1.00	0.17	2	ILF3, CARM1
Opposing (opposite direction of effect) loci:
Cyt. Band	rsID	Position (hg19)	RA/NR	MS		Psoriasis		TDMA		Heterogeneity		Colocalization Prob.		Nearby Genes
				OR	P	OR	P	OR	P	Q	P	COLOC PP	SuSiE #
1p36.11	rs6672420	25291010	A/T	1.07	2.2×10−5	0.86	8.8×10−15	1.11	6.3×10−18	2.9×10−3	0.96	0.93	3	RUNX3
2p16.1	rs1177213	61079090	A/G	0.93	4.6×10−6	1.16	2.1×10−15	1.11	5.2×10−18	3.0×10−3	0.96	0.73	6	REL * , PUS10 *
5q31.1	rs3843503	131466629	T/A	1.08	1.9×10−5	0.92	2.1×10−5	1.08	1.6×10−9	1.5×10−6	1.00	0.68	3	CSF2, P4HA2 *
6p22.1	rs1611653	29841702	G/C	1.31	3.9×10−50	0.73	1.5×10−61	1.34	6.4×10−109	1.5×10−3	0.97	-	-	HLA-B * /C, TNF
6q23.3	rs7746779	138154501	A/G	0.90	8.8×10−7	1.15	1.1×10−9	1.13	1.1×10−14	7.8×10−4	0.98	3.2×10−3	0	TNFAIP3, WAKMAR2
6q25.3	rs2451279	159515077	G/A	1.10	6.4×10−8	0.91	3.6×10−6	1.10	1.8×10−12	4.3×10−6	1.00	2.6×10−3	2	TAGAP *
7q36.1	rs10243355	150356318	G/A	1.09	3.4×10−5	0.89	1.8×10−5	1.10	3.4×10−9	6.2×10−4	0.98	0.81	1	GIMAP2 * /6 *
10q22.3	rs1250565	81047015	A/G	1.12	1.0×10−10	0.89	3.3×10−9	1.12	2.1×10−18	2.4×10−5	1.00	0.83	2	ZMIZ1 *
11p11.2	rs12574410	47169228	C/G	1.11	3.9×10−6	0.90	9.3×10−5	1.11	1.5×10−9	1.3×10−5	1.00	0.88	0	MYBPC3 * , AGBL2 *
16p13.13	rs3862471	11113463	G/T	1.17	3.2×10−23	0.92	6.4×10−6	1.14	1.3×10−25	3.0×10−3	0.96	0.85	0	CLEC16A *
22q12.3	rs5756405	37310954	A/G	1.07	2.4×10−5	0.93	4.3×10−5	1.07	4.3×10−9	4.7×10−5	0.99	0.76	3	CSF2RB * , NCF4

^*eQTL evidence in eQTLGen or GTEx v8