Table 2.

Association results for SNPs that met P < 0.05 after permutation in the analysis of craniofacial size and shape

Traita	Marker	Gene/locus	Alleles	Frequency of A1	RSQR	Effect	SE	P-value	Permuted P-value
Width of eye region
psL-psR: left-to-right palpebrale superius distance	rs17101923	HMGA2	G/T	0.78	0.9645	0.11	0.028	0.00011	0.0042
piL-piR: left-to-right palpebrale inferius distance	rs17101923	HMGA2	G/T	0.78	0.9645	0.109	0.028	0.00012	0.0049
exR.yz: distance of the right exocanthion from the YZ plane	rs17101923	HMGA2	G/T	0.78	0.9645	0.099	0.028	0.00043	0.018
enL.yz: distance of the left endocanthion from the YZ plane	rs17101923	HMGA2	G/T	0.78	0.9645	0.096	0.028	0.00067	0.025
enL-enR: left-to-right endocanthion distance	rs17101923	HMGA2	G/T	0.78	0.9645	0.094	0.028	0.00074	0.028
exL-exR: left-to-right exocanthion distance	rs17101923	HMGA2	G/T	0.78	0.9645	0.093	0.028	0.00087	0.033
Width of lower part of nose
prn-alL: pronasale to left alare distance	rs17101923	HMGA2	G/T	0.78	0.9645	0.08	0.025	0.0013	0.044
sn-alL: subnasale to left alare	rs7924176	ADK VCL AP3M1	A/G	0.58	0.9714	0.071	0.022	0.0013	0.049
alL-alR: left-to-right alare distance	rs17101923	HMGA2	G/T	0.78	0.9645	0.078	0.024	0.0014	0.048
Height and prominence of the mid-brow
g-men: glabella to mid-endocanthion distance	rs997154	AJUBA	G/A	0.23	0.9698	0.104	0.027	0.00016	0.0069

All alleles are on the forward strand. The effect allele is displayed in bold font and in each case is also the allele associated with increased the number of teeth at 12 months. Freq1 is the allele frequency of the effect allele.

^aSee Supplementary Material Figure S4 for additional information on landmark positions.