Table 1. SNPs associated with skull phenotypes (PCs).

Columns of the table show the SNP with the lowest p-value per QTL, its base-pair position, p-value calculated in GEMMA, and the proportion of total skull shape variation explained by the SNP (%varSkull).

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