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Table 1 Summary of T1D association results for the case-control collection

From: Evidence of association with type 1 diabetes in the SLC11A1 gene region

     Allele or genotype
frequency N (%)
   
Variant
[Synonym]
Location
Number of
cases
Number of
controls
Allele or
genotype
in cases in controls OR (95% C.I.) P-value
rs4674297 G > A 8502 10071 A 3710 (21.82) 4682 (23.25) 0.91 (0.86-0.96) 1.57 × 10-4
5' of SLC11A1         
within MGC50811 (aka C2orf62)    G/G 5210 (61.28) 5945 (59.03) 1.00 (reference)  
    G/A 2874 (33.80) 3570 (35.45) 0.91 (0.86-0.97)  
P HWE = 0.050    A/A 418 (4.92) 556 (5.52) 0.84 (0.74-0.96)  
Microsatellite (GT)n 3 > 2 7697 7371 2 3999 (25.98) 4010 (27.20) 0.94 (0.89-0.99) 0.016
Promoter         
    3*/3* 4195 (54.50) 3913 (53.09) 1.00 (reference)  
    3*/2 3005 (39.04) 2906 (39.42) 0.96 (0.89-1.03)  
P HWE = 0.697    2/2 497 (6.46) 552 (7.49) 0.85 (0.74-0.97)  
rs7573065 C > T 5649 6233 T 647 (5.73) 732 (5.87) 0.97 (0.87-1.09) 0.662
[-237 C->T]         
Promoter    C/C 5018 (88.83) 5518 (88.53) 1.00 (reference)  
    C/T 615 (10.89) 698 (11.20) 0.97 (0.86-1.09)  
P HWE = 0.303    T/T 16 (0.28) 17 (0.27) 1.00 (0.50-2.00)  
rs2276631 C > T 5578 6048 T 2933 (26.29) 3331 (27.54) 0.93 (0.87-0.99) 0.016
[274 [C/T]]         
Exon 3    C/C 2998 (53.75) 3153 (52.13) 1.00 (reference)  
    C/T 2227 (39.92) 2459 (40.66) 0.94 (0.87-1.02)  
P HWE = 0.144    T/T 353 (6.33) 436 (7.21) 0.84 (0.72-0.98)  
rs3731865 G > C 8787 10611 C 4691 (26.69) 6116 (28.82) 0.90 (0.86-0.94) 1.55 × 10-6
[469 +14 [G/C]; INT4]         
Intron 4    G/G 4713 (53.64) 5401 (50.90) 1.00 (reference)  
    G/C 3457 (39.34) 4304 (40.56) 0.91 (0.86-0.97)  
P HWE = 0.242    C/C 617 (7.02) 906 (8.54) 0.78 (0.69-0.87)  
rs2279015 G > A 5549 5872 A 4312 (38.85) 4658 (39.66) 0.96 (0.91-1.02) 0.205
[1465-85 [A/G]]         
Intron 13    G/G 2060 (37.12) 2142 (36.48) 1.00 (reference)  
    G/A 2666 (48.04) 2802 (47.72) 1.00 (0.92-1.08)  
P HWE = 0.817    A/A 823 (14.83) 928 (15.80) 0.92 (0.82-1.03)  
rs17235409 G > A 5498 6062 A 241 (2.19) 216 (1.78) 1.28 (1.06-1.55) 0.010
[D543N]         
Exon 15    G/G 5259 (95.65) 5849 (96.49) 1.00 (reference)  
    G/A 237 (4.31) 210 (3.46) 1.31 (1.08-1.59)  
P HWE = 0.430    A/A 2 (0.04) 3 (0.05) 0.72 (0.12-4.37)  
rs17235416 TGTG> del 8463 9835 del 312 (1.84) 299 (1.52) 1.22 (1.04-1.44) 0.015
[1729+55del4 [TGTG]; 3'UTR]         
3'UTR    TGTG/TGTG 8153 (96.34) 9539 (96.99) 1.00 (reference)  
    TGTG/del 308 (3.64) 293 (2.98) 1.24 (1.05-1.46)  
P HWE = 0.624    del/del 2 (0.02) 3 (0.03) 0.69 (0.11-4.20)  
rs1059823 A > G 5,605 6,137 ND ND ND ND   ND
[1801+86[A/G]]         
3'UTR         
P HWE = 0.001         
rs1809231 C > G 5643 6151 G 4870 (43.15) 5399 (43.89) 0.97 (0.92-1.02) 0.028**
3' intergenic region         
    C/C 1783 (31.60) 1959 (31.85) 1.00 (reference)  
    C/G 2850 (50.51) 2985 (48.53) 1.04 (0.96-1.14)  
P HWE = 0.249    G/G 1010 (17.90) 1207 (19.62) 0.91 (0.82-1.01)  
  1. Association of alleles and genotypes were tested using single locus logistic regression.
  2. * Rare microsatellite alleles (with frequency <0.1%) were combined with the common allele 3. ** The multiplicative allelic effects model was an appropriate model for all variants (P > 0.05), except for rs1809231 C>G where a genotype effects model was required (P = 0.019). [P HWE = Hardy- Weinberg equilibrium in controls; OR = odds ratio; 95% C.I. = 95% confidence intervals; ND = not done.]