Table 4.
Frequency distribution and case-control association analysis of common variants in the NTRK3 gene
| Loc (Build 36.2) | Regiona,b | Variant | rs ID | Group | Genotype Counts | Allele Counts (Frequencies) | p-valued | |||
|---|---|---|---|---|---|---|---|---|---|---|
| Maj/Maj | Het | Min/Min | Major | Minor | ||||||
| 86 528 755 | Intron 2 | T/A | rs4887380 | Cases | 107 | 62 | 7 | 276 (0.784) | 76 (0.216) | 0.063 |
| Controls | 120 | 53 | 3 | 293 (0.832) | 59 (0.168) | |||||
| 86 528 340 | Intron3 | G/C | rs4887379 | Cases | 100 | 66 | 10 | 266 (0.756) | 86 (0.244) | 0.008 |
| Controls | 120 | 53 | 3 | 293 (0.832) | 59 (0.168) | |||||
| 86 527 590 | Intron 4 | C/T | Novel | Cases | 111 | 59 | 6 | 281 (0.798) | 71 (0.202) | 0.386 |
| Controls | 108 | 61 | 2 | 277 (0.810) | 65 (0.190) | |||||
| 86 489 658 | Intron 5 | A/G | rs6496463 | Cases | 36 | 92 | 45 | 164 (0.474) | 182 (0.526) | 0.048 |
| Controls | 55 | 79 | 41 | 189 (0.540) | 161 (0.460) | |||||
| 86 481 688 | Exon6 | AAC→AAT (synonymous Asn) | rs1128994 | Cases | 94 | 70 | 12 | 258 (0.733) | 94 (0.267) | 0.466 |
| Controls | 92 | 76 | 8 | 260 (0.739) | 92 (0.261) | |||||
| 86 470 386 | Intron 12 | C/G | rs3825882c | Cases | 38 | 93 | 44 | 169 (0.483) | 181 (0.517) | 0.034 |
| Controls | 60 | 73 | 41 | 193 (0.555) | 155 (0.445) | |||||
| 86 392 534 | Intron 12 (cons 6) | G/T | rs28565987 | Cases | 138 | 34 | 2 | 310 (0.891) | 38 (0.109) | 0.431 |
| Controls | 141 | 34 | 1 | 316 (0.898) | 36 (0.102) | |||||
| 86 377 189 | Exon13 | CGC→CGG (synonymous Arg) | rs2229910 | Cases | 67 | 85 | 24 | 219 (0.622) | 133 (0.378) | 0.173 |
| Controls | 79 | 74 | 23 | 232 (0.659) | 120 (0.341) | |||||
| 86 322 455 | Intron 13 (Exon 15 of NTRK3c-3′UTR) | G/A | Novel | Cases | 156 | 17 | 2 | 329 (0.940) | 21 (0.060) | 0.556 |
| Controls | 156 | 19 | 1 | 331 (0.940) | 21 (0.060) | |||||
| 86 322 284 | Intron 13 (Exon 15 of NTRK3c-3′UTR) | G/C | rs28521337 | Cases | 37 | 92 | 47 | 166 (0.472) | 186 (0.528) | 0.530 |
| Controls | 41 | 84 | 51 | 166 (0.472) | 186 (0.528) | |||||
| 86 230 145 | Intron 16 | T/C | Novel | Cases | 152 | 24 | 0 | 328 (0.932) | 24 (0.068) | 0.616 |
| Controls | 153 | 21 | 2 | 327 (0.929) | 25 (0.071) | |||||
| 86 230 080 | Intron 16 | T/C | rs11633200 | Cases | 17 | 86 | 73 | 120 (0.341) | 232 (0.659) | 0.290 |
| Controls | 26 | 76 | 74 | 128 (0.364) | 224 (0.636) | |||||
| 86 224 467 | Intron 18 | G/A | rs1560975c | Cases | 23 | 88 | 65 | 134 (0.381) | 218 (0.619) | 0.630 |
| Controls | 23 | 81 | 67 | 127 (0.371) | 215 (0.629) | |||||
a
Regions are in reference to the NTRK3a transcript except where the NTRK1c transcript is specified.
b
“cons” refers to highly conserved regions that are numbered in accordance with their location beginning from the 5′ end of NTRK3.
c
Genotype data from Hap Map project available at www.hapmap.org.
d
Uncorrected p-values < 0.05 are marked in bold.