Table 3. Top 25 SNPs resulting from the mixed model analysis for PC2.

SNP	Chr.	Position	Alleles	Minor allele	MAF	Genotypesa	P HWEb	P mixed	Gene regionc	Pos. Rel. gened
rs10499138	6	128 533 875	A/T	A	0.253561	30/118/203	0.0473	1.70E−06	Receptor-type tyrosine-prot phosphatase kappa precursor (EC 3.1.3.48)	Intron
rs10491923	9	76 139 000	A/G	A	0.365672	49/147/139	0.3460	2.79E−05	Nuclear receptor ROR-beta (nuclear receptor RZR-beta)	Upstream
rs10499136	6	128 419 828	A/C	C	0.296296	36/136/179	0.2002	3.58E−05	Receptor-type tyrosine-prot phosphatase-kappa precursor (EC 3.1.3.48)	Intron
rs9308868	2	103 727 852	C/T	C	0.268895	25/135/184	1.0000	6.45E−05	U3 small nucleolar RNA	Upstream
rs1555167	6	62 465 026	G/T	T	0.398860	57/166/128	0.8239	9.62E−05	KH dom-containing, RNA-binding signal transduction-associated prot-2	Intron
rs9294311	6	62 470 112	C/T	T	0.398860	57/166/128	0.8239	9.62E−05	KH dom-containing, RNA-binding, signal transduction-associated prot-2	Intron
rs9294314	6	62 470 480	A/G	G	0.398860	57/166/128	0.8239	9.62E−05	KH dom-containing, RNA-binding, signal transduction-associated prot-2	Intron
rs10485162	6	128 639 684	C/T	T	0.145299	12/78/261	0.0530	0.000122	Receptor-type tyrosine-prot phosphatase-kappa precursor (EC 3.1.3.48)	Intron
rs514878	5	73 705 460	A/G	A	0.058405	2/37/312	0.3294	0.000132	Ectoderm-neural cortex 1 protein (ENC-1)	Downstream
rs10520939	5	27 970 143	C/T	T	0.082813	5/43/272	0.0516	0.000149	U6 spliceosomal RNA	Downstream
rs1201494	6	62 547 842	A/G	A	0.398571	56/167/127	0.9116	0.000165	KH dom-containing, RNA-binding, signal transduction-associated prot-2	Intron
rs304408	18	1 095 249	A/G	G	0.245588	28/111/201	0.0288	0.000175	Putative C18 or f2 variant-3	Downstream
rs768166	10	8 087 556	A/C	C	0.228198	18/121/205	1.0000	0.000175	Transcription initiation factor TFIID subunit-3	Intron
rs304409	18	1 096 342	A/G	A	0.246356	25/119/199	0.2439	0.000180	Pituitary adenylate cyclase-activating polypeptide precursor (PACAP)	Downstream
rs4936417	11	117 409 046	A/G	G	0.200000	20/100/230	0.0460	0.000202	Eukaryotic-type signal recognition particle RNA	Upstream
rs4386936	8	135 859 109	A/C	C	0.219373	15/124/212	0.6414	0.000221	Zinc finger prot 406 (Protein ZFAT)	Upstream
rs211004	5	161 577 376	C/T	T	0.370640	53/149/142	0.2033	0.000222	Gamma-aminobutyric-acid receptor gamma-2 subunit precursor	Downstream
rs522914	6	62 592 457	A/T	A	0.400285	57/167/127	0.9115	0.000224	KH dom-containing, RNA-binding, signal transduction-associated prot-2	Intron
rs565795	6	62 597 708	A/G	G	0.400285	57/167/127	0.9115	0.000224	KH dom-containing, RNA-binding, signal transduction-associated prot-2	Intron
rs265360	6	129 579 569	A/G	A	0.272727	33/120/188	0.0404	0.000247	Laminin-alpha-2 chain precursor (laminin M-chain)	Intron
rs9312176	4	67 882 411	A/G	A	0.456522	74/167/104	0.6647	0.000254	Similar to interferon-induced transmembrane prot-3	Downstream
rs1544044	20	14 459 168	C/T	T	0.465318	72/178/96	0.5892	0.000257	OTTHUMP00000030317	Intron
rs10493937	1	101 115 238	A/T	A	0.472934	85/162/104	0.1650	0.000267	Exostosin-like-2 (EC 2.4.1.223)	Intron
rs1358815	6	57 471 407	G/T	G	0.464183	73/178/98	0.6680	0.000274	DNA primase large subunit (EC 2.7.7.-)	Intron
rs6489314	12	1 627 431	A/C	A	0.341642	47/139/155	0.0916	0.000300	Adiponectin receptor prot-2	Upstream

Abbreviations: Chr., chromosome; dom, domain; MAF, minor allele frequency; P HWE, P-value resulting after Hardy–Weinberg equilibrium testing; P Mixed, P-value resulting mixed-model analysis (indicated in bold); Pos. Rel. Gene, position of the SNP relative to the gene listed in the previous column; prot, protein.

^aThe number of homozygotes for the minor allele/the number of heterozygotes/the number of homozygotes for the major allele.

^bThe Hardy–Weinberg equilibrium P-value should be larger than 0.001 for the SNP genotyping to be valid.

^c‘/' indicates that this SNP was not located within a gene region.

^d‘Upstream' or ‘Downstream' was based on the Affymetrix annotation.