Table 1.
Summary of T1D association results for the case-control collection
| 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) | ||||
| PHWE = 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) | ||||
| PHWE = 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) | ||||
| PHWE = 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) | ||||
| PHWE = 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) | ||||
| PHWE = 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) | ||||
| PHWE = 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) | ||||
| PHWE = 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) | ||||
| PHWE = 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 | ||||||||
| PHWE = 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) | ||||
| PHWE = 0.249 | G/G | 1010 (17.90) | 1207 (19.62) | 0.91 | (0.82-1.01) | |||
Association of alleles and genotypes were tested using single locus logistic regression.
* 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). [PHWE = Hardy- Weinberg equilibrium in controls; OR = odds ratio; 95% C.I. = 95% confidence intervals; ND = not done.]