Table 1. SNPs associated with skull phenotypes (PCs).
Region | Skull | Chr | Pos | SNP | p-value | %varSkull | Candidate genes |
---|---|---|---|---|---|---|---|
1 | PC1 | 11 | 32367260 | rs258942042 | 9.13E-07 | 0.75 | Sh3pxd2b |
2 | PC1 | 13 | 110231696 | rs245694506 | 3.93E-07 | 0.86 | Rab3c, Plk2, Pde4d |
3 | PC2 | 8 | 80889309 | rs228570244 | 7.54E-07 | 0.62 | Gab1, Inpp4b |
4 | PC3 | 5 | 111328046 | rs33702397 | 2.18E-27 | 2.05 | Mn1 |
5† ** | PC4 | 9 | 99713529 | rs30491142 | 9.69E-09 | 0.44 | Cldn18 |
6** | PC5 | 2 | 33284278 | rs27194486 | 5.74E-07 | 0.35 | Lmx1b |
7† ** | PC5 | 9 | 98588137 | rs13466556 | 4.35E-09 | 0.56 | Foxl2 |
8* | PC6 | 5 | 111626960 | rs254983846 | 1.53E-08 | 1.27 | Mn1 |
9* | PC6 | 19 | 4165856 | rs37378594 | 3.24E-08 | 0.48 | - |
10† * | PC7 | 13 | 31734894 | cfw-13-31734894 | 4.00E-09 | 0.53 | Foxf2, Foxc1 |
11† * | PC8 | 3 | 98931976 | rs30352013 | 4.71E-07 | 0.38 | Tbx15 |
12* | PC8 | 5 | 110918274 | rs227631022 | 2.63E-09 | 1.15 | Mn1 |
13 | PC12 | 11 | 32423285 | rs26862534 | 9.48E-07 | 0.40 | Sh3pxd2b |
14* | PC19 | 11 | 95634099 | rs26992385 | 8.83E-07 | 0.20 | - |
15 | PC20 | 2 | 83096089 | rs46747509 | 9.08E-07 | 0.61 | Itgav |
16* | PC20 | 11 | 94881746 | rs50079241 | 1.29E-07 | 0.47 | Col1a1, Dlx3 |
17* | PC22 | 15 | 11384042 | rs31584944 | 9.85E-07 | 0.25 | Npr3 |
Principal component (PC). %varSkull is the proportion of variation in skull shape explained by the SNP. This value was calculated in a multivariate regression of shape on the SNP genotype. The candidate genes were identified based on their role in bone morphogenesis (see methods). Empty cells (-) mean no compelling candidate gene emerged. The total set of genes in the QTL regions is shown in S4Table
† Regions that overlap with Maga et al 2015
* Regions that overlap with Attanasio et al 2014 using a window of 500Kb around the focal SNP
** Regions that overlap with Attanasio et al 2014 using a window of 1Mb around the focal SNP