Table II.

Non-synonymous SNPs found in LD (r² > 0.8) with 15 T1D loci.

ID	T1D SNPs	Gene	NS variants in LD (r2 > 0.8)	P- value of T1D SNP	P-value of best NS SNP
1	rs2269241	PGM1	rs11208257	3.6×10−7^	1.6×10−6^
2	rs2476601	PTPN22	rs2476601	1.35×10−27	1.35×10−27
7	rs6546909	MOGS MRPL53 TTC31 LBX2	rs2268416, rs1063588 rs1047911 rs6707475 rs17009998	6.3×10−3^	8.7×10−3^
10	rs1990760	IFIH1	rs1990760	7.43×10−5	7.43×10−5
11	rs231727	CTLA4	rs231775	4.28×10−5	4.28×10−5
16	rs6897932	IL7R	rs6897932	0.002	0.002
32	rs10877012	TSFM	rs1599932	0.44	n/a
33	rs3184504	SH2B3	rs3184504	2.11×10−9	2.11×10−9
40	rs3825932	CTSH	rs1036938	0.19	0.13
41	rs416603	TNP2	rs11640138	0.01	0.02
42	rs4788084, rs9924471	APOBR SULT1A2 SH2B1	rs180743 rs1059491, rs10797300 rs7498665	0.0006, 0.44	6.44×10−5
45	rs2290400	ZPBP2 GSDMB	rs11557467 rs2305480, rs2305479	0.007	0.006
48	rs763361	CD226	rs763361	8.07×10−5	8.07×10−5
49	rs2304256	TYK2	rs2304256	0.02	0.02
52	rs2281808	SIRPG	rs6043409	0.0009	0.001
55	rs229541	C1QTNF6	rs229527	0.05	0.04

ID: T1D loci identifiers as in Table I. Genes SULT1A2 and GSDMB, the SNPs cause deleterious changes. The best NS SNP is underlined where possible.

^{^}Association p-values are derived from Barrett et al. (2).

n/a – SNP genotypes not available.