Table 2. Top 25 SNPs resulting from the mixed-model analysis for PC1.

SNP	Chr.	Position	Alleles	Minor allele	MAF	Genotypesa	P HWEb	P Mixed	Gene regionc	Pos. Rel. gened
rs1413042	13	38 600 755	C/T	C	0.228916	24/104/204	0.0432	2.91E−05	Similar to RIKEN cDNA 8030451K01 (LOC387921)	Downstream
rs1016111	6	14 121 677	C/G	C	0.367521	49/160/142	0.7308	5.86E−05	CD83 antigen precursor (cell-surface protein HB15)	Upstream
rs1826882	15	19 989 036	A/C	C	0.113506	1/77/270	0.1024	9.41E−05	/	/
rs854273	1	69 016 062	G/T	T	0.247863	18/138/195	0.3898	0.000115	DEP domain containing-1	Upstream
rs2825601	21	19 766 620	A/G	A	0.336182	39/158/154	0.9054	0.000134	/	/
rs1988145	5	92 258 480	A/C	A	0.228228	25/102/206	0.0195	0.000144	COUP transcription factor 1 (COUP-TF1)	Upstream
rs9311746	3	60 015 052	C/T	T	0.381766	50/168/133	0.8221	0.000144	Bis(5′-adenosyl)-triphosphatase (EC 3.6.1.29)	Intron
rs161927	3	7 813 242	A/G	G	0.065407	3/39/302	0.1663	0.000149	Metabotropic glutamate receptor-7 precursor (GRM7)	Downstream
rs1358520	2	181 148 326	C/T	T	0.195157	9/119/223	0.1738	0.000187	Ubiquitin-conjugating enzyme E2 E3 (EC 6.3.2.19)	Upstream
rs2148418	13	38 564 233	A/G	G	0.215714	20/111/219	0.2675	0.000194	Similar to RIKEN cDNA 8030451K01 (LOC387921)	Downstream
rs1661609	7	52 720 759	A/T	T	0.150000	7/91/252	0.8359	0.000208	/	/
rs572619	11	115 738 853	A/T	T	0.361823	45/164/142	0.9080	0.000211	BUD13 homologue	Downstream
rs10510777	3	55 212 778	A/G	G	0.472934	76/180/95	0.6684	0.000227	Calcium channel, voltage-dependent, alpha-2/delta-3 subunit	Downstream
rs2182406	10	129 456 655	C/T	T	0.133903	8/78/265	0.4864	0.000231	Transmembrane protein-12	Downstream
rs9301169	13	106 353 066	C/T	C	0.250712	21/134/196	0.8870	0.000234	/	/
rs1388654	1	68 985 603	A/G	G	0.295714	26/155/169	0.3039	0.000249	DEP domain containing-1	Upstream
rs3751591	15	49 394 002	A/G	G	0.148415	14/75/258	0.0100	0.000250	Cytochrome P450 19A1 (EC 1.14.14.1)	Intron
rs7620394	3	55 206 368	C/T	C	0.304843	33/148/170	0.9003	0.000253	Leucine-rich repeats and transmembrane domains-1	Upstream
rs10503920	8	32 548 231	A/G	G	0.274929	34/125/192	0.0454	0.000259	Neuregulin-1, sensory and motor neuron-derived factor isoform	Intron
rs10497334	2	168 549 782	A/G	A	0.081197	1/55/295	0.7146	0.000266	STE20/SPS1-related, proline–alanine-rich protein kinase (EC 2.7.11.1)	Intron
rs7357631	9	99 568 141	A/G	A	0.497151	87/175/89	1.0000	0.000282	Forkhead box protein-E1 (thyroid transcription factor-2)	Upstream
rs2055439	5	75 511 014	A/G	A	0.403458	61/158/128	0.3166	0.000292	Synaptic vesicle glycoprotein-2C	Intron
rs10515629	5	148 875 068	C/T	C	0.196581	15/108/228	0.6132	0.000303	Casein kinase-I isoform-alpha (EC 2.7.11.1)	Intron
rs2037344	8	121 088 918	C/T	C	0.348665	39/157/141	0.7191	0.000339	DEP domain containing-6	Intron
rs3912622	11	102 626 683	A/C	C	0.111748	8/62/279	0.0570	0.000355	DYNC2H1 protein	Intron

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

^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.