Table 2 

Association analyses in type 1 diabetes families and casecontrol sample sets for immunemediated disease associated polymorphisms. 

Published SNP 
Set 1 families 
Cases and controls 



MAF 
N parentchild trios (T/NT) 
P_{TDT} 
Allelic RR [95% CI] 
Genotype RR [95% CI] 
MAF 
N cases/controls 
P_{1df} 
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  


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. 

Smyth et al. BMC Medical Genetics 2006 7:20 doi:10.1186/14712350720 