Table 1.

Characteristics of T1D^a and type 2 diabetes T2D^b risk variants

Gene	Locus	CGEMS SNP	Previous reports			C GEMS controls
			risk/nonrisk allele	RR for T1D or T2Dc	risk allele frequency	risk allele frequency	HWE p value
T1D
PTPN22	lpl3	rs2476601	T/C	2.03	0.11	0.10	0.22
IFIH1	2q24	rsl990760	A/G	1.18	0.62	0.61	0.09
IL2/IL21	4q27	rs4505848d	A/G	1.20	0.66	0.66	0.69
HLA	6p21	rs9275184e	C/T	5.18	0.09	0.10	0.87
BACH2	6ql5	rs3757247f	A/G	1.13	0.46	0.46	0.36
IL2RA	10pl5	rsl2251307	C/T	1.33	0.88	0.88	0.49
PRKCQ	10pl5	rs947474	A/G	1.16	0.81	0.81	0.28
INS	llpl5	rs1004446	C/T	1.61	0.65	0.63	0.20
ERBB3	12ql3	rs1701704	C/A	1.25	0.35	0.34	0.25
C12orf30	12q24	rsl7696736	G/A	1.20	0.42	0.44	0.16
CTSH	15q24	rs2870085g	C/T	1.16	0.68	0.67	0.73
CLEC16A	16pl3	rs2903692	G/A	1.50	0.62	0.65	0.11
PTPN2	18pll	rsl893217	G/A	1.20	0.17	0.16	0.65
C1QTNF6	22pl3	rs229527h	A/C	1.11	0.40	0.43	0.85
T2D
NOTCH2	lpl3	rs2641348	G/A	1.13	0.10	0.11	0.17
THADA	2p21	rsl3414140i	C/T	1.15	0.90	0.87	0.20
PPARG	3p25	rs6802898j	C/T	1.14	0.87	0.87	0.25
ADAMTS9	3pl4	rs4411878k	C/T	1.09	0.76	0.75	0.37
IGF2BP2	3q27	rs4402960	T/G	1.14	0.32	0.32	0.42
WFS1	4pl6	rsl0012946l	C/T	1.12	0.60	0.59	0.48
CDKAL1	6p22	rs7756992	G/A	1.14	0.32	0.28	0.40
JAZF1	7pl5	rsl635852m	T/C	1.10	0.50	0.49	0.50
SLC30A8	8q24	rsl3266634	C/T	1.15	0.69	0.71	0.42
CDKN2A/B	9p2	rs2383208n	A/G	1.20	0.83	0.81	0.32
CDC123	10pl4	rsl 1257655o	T/C	1.11	0.18	0.20	0.33
HHEX/IDE	10q23	rsllll875	C/T	1.15	0.65	0.59	0.49
TCF7L2	10q25	rs7903146	T/C	1.37	0.31	0.30	0.41
KCNQ1	llpl5	rs2237892	C/T	1.29	0.93	0.94	0.13
KCNJ11	llpl5	rs5215	C/T	1.14	0.35	0.37	0.45
TSPAN8	12q21	rsl353362p	C/T	1.09	0.27	0.27	0.40
FTO	16ql2	rs8050136	A/C	1.17	0.40	0.42	0.48
HNF1B	17ql2	rs4430796	G/A	1.10	0.47	0.50	0.50

RR = Relative risk.

^aNo tagSNP available for rs3087243 (CTLA4)

^bno tagSNP available for rs10830963 (MTNR1B)

^cRRs are previously reported per-allele odds ratios for the risk allele

^dr² = 0.826 with rs17388568

^ers2647044 (from Hakonarson) was out of HWE

^fr² = 0.904 with rs11755527

^gr² = 0.926 with rs3825932

^hr² = 1.0 with rs229541

ⁱr² = 1.0 with rs7578597

^jr² = 1.0 with rs1801282

^kr² = 0.948 with rs4607103

^lr² = 1.0 with rs100010131

^mr² = 0.97 with rs864745

ⁿr² = 1.0 with rs10811661 (from Scott et al.)

^or² = 0.80 with rs12779790

^pr² = 0.955 with rs79615.