Table 2.

Leading SNPs at three loci have been established of T1D association.

CHR	dbSNP	BP (hg38)	Gene.refGene	A1	Quality Score (r2)	Genotyped	Low PRS cases versus low PRS controls				U95	P	All cases versus all controls in cohort B				U95	P	OR heterogeneity P
							MAF	n	OR	L95			MAF	n	OR	L95
a. First cohort
1	rs2476601	11,38,34,946	PTPN22	A	0.99897	Genotyped	0.08676	6118	1.87	1.594	2.194	1.55E−14	0.1112	9450	2.244	2.048	2.458	1.92E−67	0.052
6	rs9273368	3,26,58,698	HLA-DQB1	A	0.97908	Imputed	0.2586	6118	4.073	3.616	4.587	1.24E−118	0.3841	9450	6.018	5.572	6.5	< 1E−350	6.67E−08
11	rs689	21,60,994	INS	A	0.89726	Imputed	0.2572	6118	0.391	0.3354	0.4559	4.02E−33	0.2331	9450	0.4442	0.4098	0.4815	1.03E−86	0.149
b. Switched cohort
1	rs2476601	11,38,34,946	PTPN22	A	0.99897	Genotyped	0.09515	6460	2.216	1.921	2.557	1.03E−27	0.1152	9465	2.268	2.07	2.484	3.53E−69	0.789
6	rs9273368	3,26,58,698	HLA-DQB1	A	0.97908	Imputed	0.2584	6460	3.809	3.416	4.247	6.19E−128	0.376	9465	5.937	5.503	6.404	< 1E−350	5.49E−11
11	rs689	21,60,994	INS	A	0.89726	Imputed	0.259	6460	0.4553	0.3972	0.5218	1.23E−29	0.2366	9465	0.4883	0.4517	0.5279	1.54E−72	0.383
12	rs1702877	5,60,34,024	IKZF4	T	0.98704	Imputed	0.3276	6460	1.353	1.22	1.501	1.03E−08	0.3427	9465	1.366	1.282	1.455	3.59E−22	0.877

Italic values indicate the smallest P value.