Table 2.

Genotype and allele frequencies for rs33996649 and rs2476601 PTPN22 polymorphisms in healthy controls and patients with SSc from eight countries

SNP	Population		GG	GA	AA	G	A	p Value*	OR	(95% CI)
rs33996649	Spain	SSc (n=599)	0.960	0.040	0	0.979	0.0211
		Controls (n=1128)	0.932	0.068	0	0.966	0.0341	0.04¶	0.58	0.36 to 0.92
	Belgium	SSc (n=187)	0.952	0.048	0	0.976	0.0241
		Controls (n=236)	0.949	0.051	0	0.975	0.0254	0.9	0.95	0.39 to 2.27
	England	SSc (n=477)	0.956	0.042	0.002	0.977	0.0231
		Controls (n=382)	0.969	0.031	0	0.984	0.0157	0.28	1.48	0.73 to 3.01
	Germany	SSc (n=354)	0.966	0.034	0	0.983	0.0169
		Controls (n=285)	0.958	0.042	0	0.979	0.0211	0.59	0.8	0.36 to 1.8
	Italy	SSc (n=419)	0.945	0.055	0	0.973	0.0274
		Controls (n=371)	0.938	0.062	0	0.969	0.0310	0.68	0.88	0.49 to 1.59
	Netherlands	SSc (n=185)	0.959	0.041	0	0.979	0.0207
		Controls (n=263)	0.951	0.049	0	0.975	0.0247	0.72	0.83	0.32 to 2.22
	USA	SSc (n=1050)	0.947	0.053	0	0.973	0.0267
		Controls (n=693)	0.958	0.042	0	0.979	0.0209	0.28	1.28	0.81to 2.02
	Sweden	SSc (n=191)	0.974	0.026	0	0.987	0.0131
		Controls (n=280)	0.946	0.054	0	0.973	0.0268	0.15	0.48	0.17 to1.34
	Pooled†	SSc(n=3422)	0.954	0.045	0	0.977	0.0230
		Controls (n=3638)	0.947	0.053	0	0.973	0.0530
						Fixed model		0.36	0.89	0.72 to 1.12
SNP	Population		CC	CT	TT	C	T	p Value*	OR	(95% CI)
rs2476601	Spain	SSc (n=636)	0.857	0.137	0.006	0.925	0.075
		Controls (n=1128)	0.857	0.136	0.007	0.925	0.075	0.98	0.99	0.77 to 1.29
	Belgium	SSc (n=189)	0.788	0.212	0.000	0.894	0.106
		Controls (n=256)	0.859	0.129	0.012	0.927	0.073	0.08	1.51	0.95 to 2.42
	England	SSc (n=463)	0.793	0.201	0.006	0.893	0.107
		Controls (n=373)	0.853	0.147	0.000	0.926	0.074	0.04¶	1.5	1.07 to 2.12
	Germany	SSc (n=343)	0.802	0.175	0.023	0.889	0.111
		Controls (n=288)	0.774	0.212	0.014	0.880	0.120	0.62	0.92	0.65 to 1.3
	Italy	SSc (n=383)	0.890	0.104	0.005	0.943	0.057
		Controls (n=371)	0.935	0.059	0.005	0.965	0.035	0.08¶	1.68	1.02 to 2.76
	Netherlands	SSc (n=190)	0.805	0.189	0.005	0.900	0.100
		Controls (n=277)	0.819	0.177	0.004	0.908	0.092	0.68	1.1	0.7 to 1.71
	Sweden	SSc (n=175)	0.789	0.200	0.011	0.889	0.111
		Controls (n=279)	0.789	0.190	0.022	0.884	0.116	0.82	0.95	0.62 to 1.45
	Dieudé et al19‡	SSc (n=1018)	0.820	0.172	0.008	0.906	0.094
		Controls (n=1004)	0.828	0.163	0.009	0.909	0.091	0.73	1.04	0.84 to 1.28
	Gourh et al20‡	SSc (n=666)	0.787	0.203	0.011	0.888	0.112
		Controls (n=430)	0.844	0.147	0.009	0.917	0.083	0.06¶	1.39	1.03 to 1.87
	Pooled§	SSc (n=4063)	0.819	0.173	0.009	0.905	0.095
		Controls (n=4406)	0.843	0.148	0.008	0.917	0.083
						Fixed model		0.03¶	1.15	1.03 to 1.28

^*p Value for the minor allele.

^†I²=17.6%, Breslow–Day p=0.281 Q=8.49 p=0.29; The statistical power for this pooled analysis was 97%.

^‡The authors of those papers provided by personal communication the actualisation and specific data of their works.

^§I²=33.8%, Breslow–Day p=0.145 Q=12.08 p=0.15. The statistical power for this pooled analysis was 100%.

^¶False discovery rate correction p value.

SNP, single nucleotide polymorphism; SSc, systemic sclerosis.