Table 3.
TDT analysis for SNPs in and near FOXF2 gene in 216 Asian and 75 European NSCL/P trios
| SNPs | Position build 38 | Minor allele | MAF (%) | FAM | T | NT | OR (95%CI) | P Value | Bonferroni P Value | Empiric P Value |
|---|---|---|---|---|---|---|---|---|---|---|
| Asian | ||||||||||
| rs3799321 | 1391817 | C | 4.1 | 32 | 18 | 16 | 1.13 (0.57, 2.21) | 0.73 | 1 | 1 |
| rs1711968 | 1391873 | C | 22.4 | 101 | 84 | 41 | 2.05 (1.41, 2.98) | 0.00012 | 0.00072 | 0.0016 |
| rs9405473 | 1392224 | T | 2.9 | 21 | 14 | 8 | 1.75 (0.73, 4.17) | 0.2 | 1 | 0.85 |
| rs732835 | 1392765 | C | 26.0 | 119 | 92 | 52 | 1.77 (1.26, 2.49) | 0.00086 | 0.0043 | 0.005 |
| rs3823148 | 1392958 | G | 2.6 | 19 | 13 | 7 | 1.86 (0.74, 4.66) | 0.18 | 1 | 0.75 |
| rs2293783 | 1394808 | C | 23.8 | 114 | 85 | 53 | 1.60 (1.14, 2.26) | 0.00645 | 0.032 | 0.054 |
|
| ||||||||||
| European | ||||||||||
| rs1711968 | 1391873 | C | 45.6 | 32 | 17 | 22 | 0.77 (0.41, 1.46) | 0.42 | 1 | 0.98 |
| rs732835 | 1392765 | C | 20.7 | 25 | 9 | 20 | 0.45 (0.20, 0.99) | 0.041 | 0.16 | 0.063 |
| rs2293783 | 1394808 | C | 22.1 | 27 | 10 | 23 | 0.43 (0.21, 0.91) | 0.024 | 0.1 | 0.093 |
| rs1737762 | 1395878 | A | 25.2 | 27 | 20 | 14 | 1.43 (0.72, 2.83) | 0.3 | 1 | 0.95 |
*
FAM: number of informative families, T: number of transmitted alleles, NT: number of un-transmitted alleles; Empiric P Value: P values for 10,000 permutations in Haploview