Table 2

Primary statistical analysis

ChromosomeSNPGene of interestMinor alleleMAFAutoantibody-positive subjects (n = 350) vs. autoantibody-negative subjects (n = 4,814)*P
1p13.2rs2476601PTPN22A0.11131.54 (1.27–1.88)0.00002
1p31.3rs2269241PGM1C0.22940.95 (0.80–1.14)0.61488
1q31.2rs2816316RGS1C0.17681.24 (1.03–1.49)0.02159
1q32.1rs3024505IL10A0.15681.03 (0.84–1.26)0.76514
2p25.1rs15344220G0.45741.00 (0.86–1.16)0.95979
2q24.2rs1990760IF1H1C0.39760.98 (0.84–1.14)0.78124
2q33.2rs3087243CTLA4A0.39780.97 (0.84–1.13)0.73136
3p21.31rs11711054CCR5G0.30111.05 (0.89–1.23)0.56956
4p15.2rs105170860A0.28891.21 (1.04–1.42)0.01623
4q27rs4505848IL2G0.38131.00 (0.86–1.17)0.99731
5p13.2rs6897932IL7RT0.28960.92 (0.78–1.09)0.34873
6q22.32rs9388489C6orf173G0.44761.04 (0.90–1.21)0.57597
6q25.3rs1738074TAGAPT0.41310.87 (0.75–1.01)0.06579
6q23.3rs2327832TNFAIP3G0.21200.90 (0.74–1.08)0.24535
7p12.1rs4948088COBLA0.04420.62 (0.40–0.97)0.03827
7p15.2rs7804356SKAP2C0.22820.86 (0.72–1.03)0.11118
9p24.2rs7020673GLIS3C0.49391.01 (0.87–1.17)0.88838
10p15.1rs12251307IL2RAT0.12620.95 (0.76–1.19)0.66028
10p15.1rs11258747PRKCQT0.24091.11 (0.94–1.32)0.22364
10q23.31rs10509540RNLSC0.26661.00 (0.85–1.18)0.99217
11p15.5rs7111341INST0.26590.88 (0.74–1.05)0.14362
11p15.5rs1004446INSA0.37590.77 (0.66–0.90)0.00111
12p13.31rs4763879CD69A0.37891.10 (0.94–1.28)0.23606
12q13.2rs2292239ERBB3T0.32711.33 (1.14–1.55)0.00024
12q24.12rs3184504SH2B3T0.45901.38 (1.19–1.61)0.00002
14q24.1rs1465788ZFP36L1, C14orf181T0.28740.90 (0.77–1.07)0.23562
14q32.2rs4900384C14orf64G0.32471.01 (0.86–1.18)0.93607
15q25.1rs3825932CTSHT0.34700.87 (0.74–1.01)0.07539
16p11.2rs4788084IL27T0.44320.96 (0.83–1.11)0.5755
16p13.13rs12708716CLEC16AG0.34300.84 (0.72–0.99)0.03435
16q23.1rs7202877CTRB2G0.11151.12 (0.89–1.40)0.33022
17p13.1rs169569362 genesT0.11871.02 (0.82–1.28)0.84991
17q12rs2290400ORMDLT0.47180.93 (0.80–1.08)0.33644
17q21.2rs7221109CCR7T0.37101.03 (0.88–1.20)0.73972
18p11.21rs1893217PTPN2G0.16410.99 (0.81–1.20)0.90474
18q22.2rs763361CD226T0.47991.08 (0.93–1.26)0.29751
19q13.32rs425105PRKD2C0.15851.07 (0.88–1.31)0.48067
20p13rs2281808SIRPGT0.34200.94 (0.80–1.10)0.42631
21q22.3rs11203203UBASH3AA0.34621.05 (0.90–1.23)0.54469
22q12.2rs5753037HORMAD2T0.36041.09 (0.93–1.27)0.30521
22q13.1rs229541C1QTNF6A0.40961.08 (0.93–1.25)0.3356
  • Replication of 41 newly identified T1D risk loci from the T1DGC in 350 autoantibody-positive subjects vs. 4,814 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 covariates 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.