Table 2. Haplotype associations of SNPs belonging to the six LD blocks of LMX1B, in 252 trios.
Block | Haplotype* | Frequency | T(%) | Individual p- | Permutation p- | Block p- |
value† | value‡ | value | ||||
Block 1 (SNPs 01–06) | GGTATG | 0.355 | 51.67 | 0.6291 | 1 | |
GACATA | 0.25 | 48.81 | 0.7487 | 1 | ||
GACACG | 0.244 | 45.71 | 0.2568 | 0.994 | ||
AGCGTG | 0.073 | 66.13 | 0.0079 | 0.114 | ||
GACATG | 0.052 | 51.42 | 0.8461 | 1 | ||
GGTACG | 0.014 | 30.77 | 0.1658 | 0.97 | 0.096 | |
Block 2 (SNPs 08–09) | CC | 0.406 | 50.23 | 0.9432 | 1 | |
TC | 0.353 | 54.03 | 0.2242 | 0.987 | ||
TA | 0.239 | 44.23 | 0.1255 | 0.892 | 0.258 | |
Block 3 (SNPs 10–11) | CG | 0.525 | 48.4 | 0.6123 | 1 | |
TA | 0.345 | 52.71 | 0.4094 | 1 | ||
CA | 0.126 | 48.79 | 0.8046 | 1 | 0.731 | |
Block 4 (SNPs 12–16) | GGCGA | 0.379 | 53.41 | 0.3114 | 0.998 | |
GGCGG | 0.209 | 45.31 | 0.2362 | 0.991 | ||
GACCG | 0.201 | 48.99 | 0.8072 | 1 | ||
GGTCG | 0.119 | 55.41 | 0.2624 | 0.994 | ||
TGTCG | 0.071 | 48.81 | 0.8455 | 1 | 0.595 | |
Block 5 (SNPs 18–19) | AA | 0.58 | 52.42 | 0.4476 | 1 | |
GA | 0.304 | 47.25 | 0.1587 | 0.966 | ||
GG | 0.112 | 53.61 | 0.4772 | 1 | 0.354 | |
Block 6 (SNPs 20–22) | GGC | 0.35 | 55.39 | 0.111 | 0.868 | |
GAC | 0.332 | 48.19 | 0.59 | 1 | ||
GGT | 0.21 | 47.63 | 0.5365 | 1 | ||
TGC | 0.107 | 46.45 | 0.4947 | 1 | 0.512 |
T: Transmitted / (Transmitted + Untransmitted).
‡10,000 permutations.
*All possible combinations of haplotypes with frequency >0.01 †Significant p-values (<0.05) are indicated in bold italics.