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Table 2 Association analyses in type 1 diabetes families and case-control sample sets for immune-mediated disease associated polymorphisms.

From: Analysis of polymorphisms in 16 genes in type 1 diabetes that have been associated with other immune-mediated diseases

Published SNP Set 1 families Cases and controls
  MAF N parent-child trios (T/NT) PTDT Allelic RR [95% CI] Genotype RR [95% CI] MAF N cases/controls P1df Allelic OR [95% CI] Genotype OR [95% CI]
FCRL3 A>G rs7528684 0.46 901 (641/571) 0.04 0.89 [0.80–1.00] A/A 1.00 [ref] A/G 0.88 [0.75–1.04] G/G 0.79 [0.63–1.00] 0.45 1896/2020 0.97 1.00 [0.91–1.10] A/A 1.00 [ref] A/G 1.02 [0.87–1.18] G/G 0.99 [0.82–1.20]
CFH A>G rs1061170 0.38 823 (541/517) 0.46 0.96 [0.85–1.08] A/A 1.00 [ref] A/G 1.00 [0.85–1.17] G/G 0.88 [0.68–1.14] 0.38 3149/3485 0.87 0.99 [0.92–1.07] A/A 1.00 [ref] A/G 1.07 [0.96–1.19] G/G 0.94 [0.81–1.10]
SLC9A3R1 G>A rs734232 0.45 965 (644/642) 0.96 1.00 [0.90–1.12] G/G 1.00 [ref] G/A 1.03 [0.88–1.21] A/A 1.00 [0.80–1.25] 0.45 1578/1736 0.34 1.05 [0.95–1.17] G/G 1.00 [ref] G/A 0.92 [0.78–1.10] A/A 1.14 [0.92–1.41]
PADI4 C>T rs2240340 0.41 942 (610/655) 0.21 1.07 [0.96–1.20] T/T 1.00 [ref] C/T 1.07 [0.92–1.25] C/C 1.15 [0.92–1.44] 0.42 1573/1732 0.87 1.01 [0.91–1.12] T/T 1.00 [ref] C/T 1.09 [0.92–1.29] C/C 0.99 [0.80–1.23]
RUNX1 C>G rs2268277 0.34 896 (578/565) 0.70 1.02 [0.91–1.15] T/T 1.00 [ref] T/C 0.96 [0.83–1.11] C/C 1.12 [0.87–1.43] 0.36 1586/1725 0.21 0.93 [0.84–1.04] T/T 1.00 [ref] T/C 0.90 [0.76–1.05] C/C 0.90 [0.71–1.14]
SPINK5           
+316 A>C ss28514851 0.04 178 (89/91) 0.88 0.98 [0.73–1.31] A/A 1.00 [ref] A/C 0.98 [0.73–1.31] C/C 0.98 [0.10–9.55] 0.03 1540/1678 0.40 0.88 [0.66–1.18] A/A 1.00 [ref] A/C 0.88 [0.65–1.19] C/C 0.82 [0.14–4.71]
+1103 T>C rs2303064 0.48 915 (583/602) 0.58 0.97 [0.86–1.09] T/T 1.00 [ref] T/C 0.99 [0.84–1.17] C/C 0.94 [0.74–1.18] 0.47 1527/1665 0.30 0.95 [0.85–1.05] T/T 1.00 [ref] T/C 0.96 [0.80–1.14] C/C 0.89 [0.72–1.10]
+1156 G>A rs2303063 0.10 357 (196/213) 0.40 0.92 [0.76–1.12] G/G 1.00 [ref] G/A 0.93 [0.75–1.15] A/A 0.81 [0.42–1.57] 0.11 1530/1507 0.03 2 df 0.87 [0.73–1.04] G/G 1.00 [ref] G/A 0.79 [0.64–0.96] A/A 1.48 [0.72–3.03]
+1258 C>T rs2303067 0.48 947 (617/622) 0.89 0.99 [0.89–1.11] C/C 1.00 [ref] C/T 1.03 [0.87–1.22] T/T 0.98 [0.79–1.23] 0.47 1534/1641 0.36 0.95 [0.85–1.06] C/C 1.00 [ref] C/T 0.98 [0.82–1.17] T/T 0.90 [0.73–1.12]
+2475 C>A rs2303070 0.07 317 (150/186) 0.05 0.81 [0.65–1.00] C/C 1.00 [ref] C/A 0.85 [0.68–1.06] A/A 0.15 [0.02–1.13] 0.08 1479/1513 0.06 2 df 0.91 [0.73–1.12] C/C 1.00 [ref] C/A 0.82 [0.66–1.04] A/A 2.51 [0.81–7.79]
+2915 A>G ss28514856 0.04 184 (92/105) 0.35 0.88 [0.66–1.16] A/A 1.00 [ref] A/G 0.87 [0.65–1.17] G/G 0.82 [0.22–3.03] 0.03 1547/1685 0.91 0.98 [0.72–1.33] A/A 1.00 [ref] A/G 0.98 [0.72–1.33] G/G -
  1. MAF: Minor allele frequency, T: transmitted, NT: not transmitted, TDT: transmission/disequilibrium test P value, RR: relative risk, 95% CI: 95% confidence intervals, OR: odds ratio N: number.