TABLE 1.
Allele frequencies in DPT-1 participants and comparative cohorts
| Chromosome | Gene name | Polymorphism | Alleles |
rs number | Allele counts 0/1/2 |
MAF |
OR (95% CI) | P value | Control subjects MAF |
Case subjects MAF |
||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 1 | Nonprogressor | Progressor | Nonprogressor | Progressor | Lit. | HapMap CEU | DCGS | Lit. | DCGS | ||||||
| 6 | Lymphotoxin-α | +10 | G | A | rs1800683 | 137/173/39 | 115/95/17 | 0.36 | 0.28 | 1.41 (1.1–1.83) | 9.4E–03 | 0.36 | 0.34 | 0.44 | ||
| 11 | Insulin | −23 Hphl | T | A | rs689 | 16/109/221 | 7/63/153 | 0.20 | 0.17 | 1.23 (0.9–1.67) | 0.22 | 0.32 | 0.24 | 0.28 | 0.12 | 0.18 |
| 1 | PTPN22 | R620W | C | T | rs2476601 | 253/86/9 | 155/66/6 | 0.15 | 0.17 | 1.18 (0.86–1.63) | 0.35 | 0.06–0.15 | 0.14 | 0.08 | 0.15–0.17 | 0.19 |
| 10 | IL-2 Ra (CD25) | Intron 1 | G | A | rs706778 | 106/175/64 | 57/124/45 | 0.44 | 0.47 | 1.15 (0.91–1.46) | 0.28 | 00.4–0.45 | 0.45 | 0.39* | 0.45 | 0.48* |
| 10 | IL-2 Ra (CD25) | Intron 1 | T | C | rs3118470 | 145/160/41 | 85/115/26 | 0.35 | 0.37 | 1.09 (0.8–1.39) | 0.54 | 0.32–0.34 | 0.29 | 0.25* | 0.36 | 0.38* |
| 10 | IL-2 Ra (CD25) | IL-2 Ra region | C | A | rs41295061 | 307/36/5 | 194/28/1 | 0.07 | 0.07 | 1.02 (0.63–1.64) | 0.96 | 0.11 | 0.07 | |||
| 10 | IL-2 Ra (CD25) | IL-2 Ra region | T | A | rs11594656 | 204/119/20 | 141/67/13 | 0.23 | 0.21 | 1.13 (0.85–1.51) | 0.44 | 0.25 | 0.21 | 0.22 | ||
| 2 | IFIH1 | A946T | C | T | rs1990760 | 43/139/143 | 25/104/93 | 0.35 | 0.35 | 1.00 (0.78–1.29) | 0.97 | 0.39 | 0.39 | 0.35 | ||
| 1 | Fc receptor-like 3 | Prom −169 | A | G | rs7528684 | 99/174/67 | 74/107/42 | 0.45 | 0.43 | 1.11 (0.87–1.41) | 0.45 | 0.45 | 0.44 | 0.49 | 0.44 | |
| 6 | C6orf118 | M256I | C | A | rs510579 | 144/158/42 | 88/111/25 | 0.35 | 0.36 | 1.03 (0.81–1.33) | 0.84 | 0.35 | 0.36 | 0.38 | ||
| 5 | CAPSL | R75Q | A | G | rs1445898 | 55/184/94 | 41/103/68 | 0.44 | 0.44 | 1.02 (0.8–1.31) | 0.92 | 0.44 | 0.39 | 0.41 | ||
| 2 | CTLA4 | Prom −1577 | G | A | rs11571316 | 129/176/42 | 90/102/32 | 0.37 | 0.37 | 1.02 (0.8–1.3) | 0.94 | 0.42 | 0.47 | 0.46 | 0.35 | 0.42 |
| 2 | CTLA4 | Prom −318 | T | C | rs5742909 | 0/60/278 | 2/34/188 | 0.09 | 0.08 | 1.05 (0.69–1.61) | 0.90 | 0.11 | 0.06 | 0.06 | 0.09 | 0.08 |
| 2 | CTLA4 | T49A | G | A | rs231775 | 57/175/111 | 43/115/66 | 0.42 | 0.45 | 1.12 (0.88–1.42) | 0.40 | 0.43 | 0.38 | 0.38 | 0.29 | 0.42 |
| 2 | CTLA4 | 3'UTR 6230 (CT60) | G | A | rs3087243 | 117/181/48 | 84/105/35 | 0.40 | 0.39 | 1.04 (0.82–1.33) | 0.79 | 0.48 | 0.46 | 0.47 | 0.37 | 0.43 |
| 2 | CTLA4 | JO31 | C | A | rs11571302 | 101/176/47 | 74/108/38 | 0.42 | 0.42 | 1.01 (0.79–1.29) | 0.99 | 0.50 | 0.49 | 0.39 | 0.47 | |
| 2 | CD28 | Intron 1 | C | T | rs10932017 | 74/182/90 | 43/116/64 | 0.48 | 0.45 | 1.10 (0.87–1.4) | 0.47 | 0.44 | 0.42 | 0.43 | 0.45 | |
| 2 | CD28 | Intron 1 | A | T | rs2013278 | 39/145/148 | 25/98/97 | 0.34 | 0.34 | 1.00 (0.78–1.29) | 0.96 | 0.36 | 0.23 | 0.26 | ||
| 2 | CD28 | 3′UTR | G | T | rs3181113 | 313/35/0 | 211/11/1 | 0.05 | 0.03 | 1.76 (0.92–3.37) | 0.11 | 0.03 | 0.03 | 0.04 | 0.02 | |
| 2 | CD28 | 3′UTR | T | A | rs11681201 | 22/117/210 | 12/87/128 | 0.23 | 0.24 | 1.08 (0.82–1.42) | 0.64 | 0.13 | 0.20 | 0.15 | 0.18 | |
| 2 | ICOS | Prom −1817 | T | C | rs4452124 | 263/76/5 | 182/38/2 | 0.13 | 0.09 | 1.37 (0.93–2.02) | 0.14 | 0.08 | 0.06 | 0.08 | 0.07 | |
| 2 | ICOS | Intron 1 | C | T | rs4335928 | 0/79/269 | 4/52/170 | 0.11 | 0.13 | 1.20 (0.84–1.71) | 0.38 | 0.11 | 0.10 | 0.10 | 0.13 | 0.12 |
| 2 | ICOS | Intron 1 | C | T | rs4675377 | 20/146/179 | 13/92/121 | 0.27 | 0.26 | 1.04 (0.8–1.37) | 0.80 | 0.17 | 0.18 | 0.22 | 0.26 | |
| 12 | VDR | BsmI Intron3 | T | C | rs1544410 | 142/146/56 | 86/99/38 | 0.38 | 0.39 | 1.08 (0.84–1.37) | 0.60 | 0.12–0.25 | 0.44 | 0.38 | 0.12–0.23 | 0.38 |
| 4 | TLR2 | S450S | T | C | rs3804100 | 302/38/1 | 197/25/2 | 0.06 | 0.06 | 1.11 (0.68–1.82) | 0.77 | 0.41† | 0.05 | 0.07 | 0.39† | 0.07 |
| 19 | KIR 2DS3 | Abs | Pres | 252/80/0 | 158/60/0 | 0.12 | 0.14 | 1.16 (0.81–1.67) | 0.46 | 0.38 | 0.32 | 0.21 | 0.41 | |||
| 10 | TCF7L2 | Intron 3 | C | T | rs7903146 | 182/134/31 | 115/90/21 | 0.28 | 0.29 | 1.05 (0.81–1.36) | 0.78 | 0.29 | 0.25 | 0.31 | 0.41 | 0.30 |
| 8 | SLC30A8 | R325W | C | T | rs13266634 | 187/131/30 | 116/86/24 | 0.27 | 0.30 | 1.11 (0.86–1.45) | 0.46 | 0.30 | 0.25 | 0.29 | 0.25 | 0.31 |
| 10 | HHEX | HHEX region | A | G | rs7923837 | 48/160/136 | 33/112/81 | 0.37 | 0.39 | 1.10 (0.86–1.4) | 0.50 | 0.38 | 0.38 | 0.37 | 0.34 | 0.40 |
| 10 | HHEX | HHEX region | G | A | rs1111875 | 115/179/54 | 73/108/45 | 0.41 | 0.44 | 1.11 (0.87–1.41) | 0.42 | 0.40 | 0.44 | 0.39 | 0.36 | 0.41 |
| 11 | LOC387761 | Intron 5 | G | A | rs7480010 | 189/139/21 | 115/92/19 | 0.26 | 0.29 | 1.15 (0.88–1.5) | 0.32 | 0.30 | 0.25 | 0.30 | 0.34 | 0.32 |
| 11 | EXT2 | Intron 14 | A | G | rs3740878 | 200/124/21 | 119/96/11 | 0.24 | 0.26 | 1.12 (0.85–1.47) | 0.48 | 0.27 | 0.30 | 0.27 | 0.24 | 0.27 |
| 12 | ERBB2 | Intron 7 | A | C | rs2292239 | 46/191/109 | 35/100/90 | 0.41 | 0.38 | 1.14 (0.89–1.45) | 0.32 | 0.36 | 0.30 | 0.41 | ||
| 18 | PTPN2 | Intron 7 | T | C | rs1893217 | 236/101/8 | 149/62/14 | 0.17 | 0.20 | 1.22 (0.9–1.66) | 0.22 | 0.17 | 0.19 | 0.21 | ||
| 12 | SH2B3 | Exon 3 | C | T | rs3184504 | 85/168/89 | 54/111/58 | 0.49 | 0.49 | 1.01 (0.8–1.29) | 0.97 | 0.49 | 0.41 | 0.56 | ||
| 12 | C12Orf30 | Intron 15 | A | G | rs17696736 | 99/174/72 | 72/105/47 | 0.46 | 0.44 | 1.07 (0.84–1.36) | 0.62 | 0.43 | 0.35 | 0.49 | ||
| 16 | CLEC16A | Intron 19 | A | G | rs12708716 | 160/147/33 | 100/90/30 | 0.31 | 0.34 | 1.13 (0.88–1.46) | 0.37 | 0.35 | 0.29 | 0.31 | ||
*
Allele frequencies from the Diabetes in Adolescents and the Very Young (DAVY) study (31).
†
Allele frequency in Koreans. Abs, absent; MAF, minor allele frequency; Pres, present.