Table 5

Primary statistical analysis

ChromosomeSNPGene of interestMinor alleleMAFSubjects with T1D
(n = 84)
vs. all other subjects
(n = 5,080)*P
1p13.2rs2476601PTPN22A0.11132.42 (1.70–3.44)1.01 × 10−6
1p31.3rs2269241PGM1C0.22941.04 (0.73–1.49)0.81755
1q31.2rs2816316RGS1C0.17680.91 (0.60–1.37)0.64423
1q32.1rs3024505IL10A0.15680.97 (0.64–1.48)0.89277
2p25.1rs15344220G0.45741.06 (0.78–1.44)0.72504
2q24.2rs1990760IF1H1C0.39761.08 (0.79–1.46)0.63795
2q33.2rs3087243CTLA4A0.39781.20 (0.88–1.63)0.24179
3p21.31rs11711054CCR5G0.30111.40 (1.02–1.92)0.03629
4p15.2rs105170860A0.28891.25 (0.91–1.72)0.16686
4q27rs4505848IL2G0.38130.98 (0.71–1.34)0.88061
5p13.2rs6897932IL7RT0.28961.09 (0.79–1.52)0.59696
6q22.32rs9388489C6orf173G0.44760.98 (0.72–1.33)0.89509
6q25.3rs1738074TAGAPT0.41310.85 (0.62–1.15)0.29345
6q23.3rs2327832TNFAIP3G0.21201.26 (0.89–1.79)0.19154
7p12.1rs4948088COBLA0.04420.68 (0.28–1.66)0.39871
7p15.2rs7804356SKAP2C0.22820.75 (0.51–1.12)0.15947
9p24.2rs7020673GLIS3C0.49391.18 (0.87–1.60)0.28837
10p15.1rs12251307IL2RAT0.12621.07 (0.68–1.68)0.76958
10p15.1rs11258747PRKCQT0.24091.20 (0.85–1.68)0.3033
10q23.31rs10509540RNLSC0.26660.98 (0.70–1.38)0.901
11p15.5rs7111341INST0.26590.57 (0.38–0.85)0.00646
11p15.5rs1004446INSA0.37590.63 (0.45–0.88)0.0072
12p13.31rs4763879CD69A0.37890.95 (0.69–1.30)0.72972
12q13.2rs2292239ERBB3T0.32711.53 (1.13–2.08)0.0066
12q24.12rs3184504SH2B3T0.45901.40 (1.03–1.89)0.03083
14q24.1rs1465788ZFP36L1, C14orf181T0.28740.88 (0.63–1.24)0.47921
14q32.2rs4900384C14orf64G0.32470.71 (0.50–1.00)0.04973
15q25.1rs3825932CTSHT0.34700.68 (0.48–0.95)0.02483
16p11.2rs4788084IL27T0.44320.88 (0.65–1.19)0.41201
16p13.13rs12708716CLEC16AG0.34300.89 (0.64–1.23)0.47246
16q23.1rs7202877CTRB2G0.11150.85 (0.52–1.40)0.52287
17p13.1rs169569362 genesT0.11871.19 (0.77–1.84)0.42846
17q12rs2290400ORMDLT0.47180.78 (0.58–1.06)0.11691
17q21.2rs7221109CCR7T0.37101.11 (0.82–1.52)0.50186
18p11.21rs1893217PTPN2G0.16410.93 (0.62–1.40)0.7313
18q22.2rs763361CD226T0.47991.02 (0.75–1.38)0.90741
19q13.32rs425105PRKD2C0.15851.00 (0.66–1.51)0.9864
20p13rs2281808SIRPGT0.34200.81 (0.58–1.13)0.21733
21q22.3rs11203203UBASH3AA0.34621.06 (0.77–1.46)0.74207
22q12.2rs5753037HORMAD2T0.36041.20 (0.87–1.65)0.26825
22q13.1rs229541C1QTNF6A0.40960.92 (0.67–1.25)0.59161
  • Replication of 41 newly identified T1D risk loci from the T1DGC in 84 subjects with T1D vs. 5,080 autoantibody-negative subjects enrolled in the TEDDY study. Subjects eligible for TEDDY carried high-risk HLA DR-DQ genotypes. The MAF for the respective SNP was calculated from the results from all subjects. Proportional hazards models included HLA category, sex, and country for European sites as covariates. For U.S. sites, the principal components were estimated from our data from the U.S. population to be included in the model as a covariate for the two major principal components. The principal components were used to adjust for heterogeneity within the Caucasian population in the U.S. sites. FDRs and members from the same family were omitted from the analyses. Risk was estimated as HRs and 95% CIs. The factors indicating nominal significant risk or protection are indicated in bold.

  • *HR (95% CI).

  • †χ2-P values remained significant after Bonferroni correction for multiple comparison of 41 SNPs if less than 0.0012.