Table 2 Thirty SNPs associated with SSc in a meta-analysis comparing signals in European and Japanese GWASs

From: GWAS for systemic sclerosis identifies six novel susceptibility loci including one in the Fcγ receptor region

							Meta-analysis					JPN					EUR
CHR	POS	ID	Type	Gene	EA	NEA	BETA	SE	P-value	Q	I	EAF (case control)		BETA	SE	P-value	EAF	BETA	SE	P-value
Primary
1	167420425	rs2045526	intronic	CD247	G	T	−0.076	0.028	2.22E-10	0.012	84.1	0.125	0.128	−0.021	0.057	0.398	0.390	−0.092	0.032	1.31E-11
1	173243581	rs844663	ncRNA_intronic	TNFSF4/LOC100506023	C	T	0.076	0.025	4.96E-12	0.870	0	0.281	0.242	0.079	0.043	2.13E-05	0.276	0.075	0.032	5.05E-08
2	191959489	rs4853458	intronic	STAT4	A	G	0.140	0.026	1.91E-35	0.310	3.11	0.425	0.352	0.153	0.039	5.01E-19	0.231	0.129	0.035	4.86E-18
3	28074673	rs398390	intergenic	*LINC01980-CMC1-EOMES*	C	T	0.048	0.020	1.66E-08	0.846	0	0.450	0.425	0.045	0.039	0.0076	0.487	0.049	0.023	6.34E-07
3	58131515	rs7355798	intronic	FLNB	T	C	0.061	0.022	3.40E-10	0.377	0	0.076	0.066	0.088	0.073	0.0054	0.243	0.058	0.024	1.24E-08
3	119116150	rs9884090	intronic	ARHGAP31	A	G	−0.074	0.024	6.15E-13	0.469	0	0.281	0.311	−0.062	0.042	6.96.E-04	0.155	−0.078	0.029	1.89E-10
3	159733527	rs589446	ncRNA_intronic	IL12A-AS1	T	G	−0.060	0.023	8.02E-10	0.087	65.8	0.079	0.080	−0.011	0.070	0.724	0.350	−0.066	0.024	1.95E-10
4	965779	rs11724804	intronic	DGKQ	A	G	0.057	0.021	1.86E-10	0.047	74.6	0.438	0.428	0.025	0.043	0.185	0.441	0.067	0.024	5.31E-11
4	103449041	rs230534	intronic	NFKB1	T	C	0.063	0.021	4.02E-12	0.775	0	0.398	0.366	0.067	0.041	1.78.E-04	0.338	0.061	0.025	5.38E-09
5	150455732	rs3792783	intronic	TNIP1	G	A	0.069	0.023	2.15E-12	0.052	73.4	0.252	0.233	0.038	0.043	0.0439	0.158	0.081	0.027	2.42E-12
6	106568034	rs548234	intergenic	PRDM1-ATG5	C	T	0.071	0.025	8.06E-11	0.198	39.7	0.378	0.334	0.088	0.039	2.17E-07	0.314	0.059	0.034	2.86E-05
6	138195151	rs5029937	intronic	TNFAIP3	T	G	0.159	0.050	2.15E-13	0.401	0	0.102	0.070	0.175	0.063	1.67E-10	0.024	0.137	0.086	1.17E-04
6	152042260	rs10484921	intronic	*ESR1*	A	C	0.060	0.024	8.30E-09	0.083	66.6	0.150	0.124	0.095	0.053	3.58E-05	0.243	0.051	0.028	1.20E-05
7	128573967	rs4728142	intergenic	KCP-IRF5	A	G	0.092	0.027	1.61E-15	0.006	86.6	0.142	0.105	0.148	0.054	2.83E-10	0.449	0.074	0.031	2.24E-08
8	11343973	rs2736340	intergenic	FAM167A-BLK	C	T	−0.095	0.020	1.06E-26	0.832	0	0.285	0.327	−0.099	0.046	6.23E-07	0.244	0.094	0.023	3.33E-21
8	61396829	rs2013112	intergenic	LINC01301-RAB2A	T	C	−0.049	0.018	1.05E-09	0.611	0	0.385	0.411	−0.056	0.039	9.78.E-04	0.379	−0.046	0.021	2.66E-07
11	118642085	rs10892286	intronic	DDX6	C	A	−0.066	0.024	1.31E-10	0.053	73.3	0.115	0.123	−0.020	0.060	0.447	0.201	−0.075	0.026	2.12E-11
14	105407208	rs11851053	exonic	AHNAK2*	C	T	−0.053	0.032	1.70E-11	0.000	94.2	0.322	0.380	−0.116	0.042	2.81E-11	0.466	−0.037	0.056	2.27E-05
15	75077367	rs1378942	intronic	CSK	A	C	−0.066	0.020	9.15E-15	0.159	49.6	0.186	0.197	−0.039	0.048	0.0626	0.387	−0.071	0.022	1.84E-14
16	85971922	rs11117420	intergenic	IRF8-LINC01082	C	G	−0.094	0.025	1.42E-17	0.970	0	0.096	0.119	−0.095	0.065	6.97.E-04	0.195	−0.094	0.028	3.82E-15
17	38063381	rs883770	intronic	GSDMB	T	C	0.048	0.018	1.17E-09	0.412	0	0.278	0.260	0.035	0.042	0.0564	0.498	0.051	0.021	4.79E-09
17	73224639	rs1005714	intronic	NUP85	G	C	−0.065	0.026	9.59E-09	0.399	0	0.151	0.158	−0.042	0.069	0.166	0.200	−0.069	0.029	1.87E-08
19	18193191	rs2305743	intronic	IL12RB1	A	G	−0.062	0.025	2.37E-08	0.005	87.5	0.213	0.229	−0.012	0.048	0.579	0.199	−0.081	0.031	4.64E-10
20	44688665	rs9074	UTR3	SLC12A5**	A	G	0.050	0.021	2.21E-08	0.826	0	0.344	0.321	0.054	0.040	0.0018	0.260	0.049	0.025	3.35E-06
Secondary
1	173318664	rs10912594	ncRNA_intronic	TNFSF4/LOC100506023	C	G	−0.062	0.021	6.41E-12	0.980	0	0.309	0.329	−0.062	0.050	0.002085	0.3439	−0.062	0.023	8.13E-10
2	191940451	rs7601754	intronic	STAT4	A	G	−0.072	0.027	1.14E-09	0.155	50.6	0.136	0.180	−0.102	0.058	2.03E-05	0.1809	−0.062	0.031	4.75E-06
3	58375286	rs4076852	intronic	PXK	A	G	0.051	0.021	1.25E-08	0.036	77.3	0.262	0.255	0.014	0.049	0.463	0.2604	0.061	0.023	1.71E-09
6	106734040	rs633724	intronic	ATG5	T	C	0.044	0.018	2.48E-08	0.257	22.1	0.504	0.492	0.028	0.040	0.0858	0.3549	0.049	0.021	5.87E-08
7	128722514	rs17340646	intergenic	TPI1P2-LOC407835	G	T	0.080	0.033	1.94E-08	0.830	0	0.0181	0.0175	0.097	0.204	0.241	0.2078	0.079	0.033	3.84E-08
Tertiary
2	191534372	rs16832798	intronic	NAB1	C	T	0.050	0.023	5.15E-07	0.2394	27.8	0.499	0.490	0.034	0.040	0.0377	0.1481	0.059	0.029	2.37E-06

Inverse-variance fixed effect model was utilized for a meta-analysis of Japanese (1428 cases and 112,599 controls) and European (9095 cases and 17,584 controls) GWAS datasets.
JPN Japanese, EUR European, CHR chromosome, POS genomic position in GRCh37 coordinate, EA effect allele, NEA non-effect allele, EAF effect allele frequency, BETA beta coefficient of logistic regression, SE standard error; * synonymous SNV. AHNAK2:NM_001350929:exon7:c.A14280A:p.V4760V,AHNAK2:NM_138420:exon7:c.A14580A:p.V4860V; ** NM_001134771:c.*2421 A > G,NM_020708:c.*2421 A > G;; gene symbols are indicated in italics;the novel disease-associated SNPs are hilighted with bold.

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Table 2 Thirty SNPs associated with SSc in a meta-analysis comparing signals in European and Japanese GWASs

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