Table 2. Gene discovery using EigenGWAS.

Gene	Lead SNP	Position	Allele	P-valuea	MAF (TSI:CEU)	Fstb	Annotation
CEU and TSI samples
LCT	rs6719488	2:135817629	G/T	6.68e−34 (1.21e−20)	0.733:0.206	0.558	Lactose persistent locus
DARS	rs13404551	2:135964425	C/T	8.18e−39 (1.51e−23)	0.756:0.206	0.604	Genetic hitchhiking because of LCT
MICA	rs2256175	6:31412672	T/C	8.94e−10 (2.60e−6)	0.665:0.360	0.183	MHC class I polypeptide-related sequence A
HIF1A	rs2256205	14:61670944	A/G	1.51e−10 (8.86e−7)	0.464:0.179	0.192	HIF-1A thus plays an essential role in embryonic vascularization, tumour angiogenesis and pathophysiology of ischaemic disease.
HERC2	rs8039195	15:26189679	C/T	2.75e−12 (8.22e−08)	0.403:0.122	0.212	Genetic variations in this gene are associated with skin/hair/eye pigmentation variability
Gene	Lead SNP	Position	Allele	P-valuea	MAF (Southern Europeans: Northern Europeans)	Fstb	Annotation
POPRES European samples
LCT	rs3754686	2:135817629	T/C	3.30e−106 (1.23e−22)	0.514:0.279	0.110
DARS	rs13404551	2:135964425	C/T	6.32e−102 (8.99e−22)	0.518:0.293	0.106
SLC4A4	rs605203	6:31819235	C/A	8.94e−44 (5.77e−10)	0.214:0.343	0.040	Defects in this gene can cause sialidosis, a lysosomal storage disease
HERC2	rs1667394	15:26189679	C/T	3.90e−38 (8.15e−09)	0.276:0.173	0.041

Abbreviations: GWAS, genome-wide association study; MAF, minor allele frequency; SNP, single-nucleotide polymorphism.

The P-value cutoff for CEU and TSI was 5.44e−08 (919 133 SNPs) and for POPRES was 7.76e−08 (643 995 SNPs) at genome-wide significance level of α=0.05. λ_GC=1.725 for CEU and TSI and λ_GC=5.00 for POPRES.

^aP-values without λ_GC correction, and with λ_GC correction in parentheses.

^bF_st is calculated by partitioning the sample into two groups upon E₁ >0. For TSI and CEU set, partitioning on E₁ perfectly separated TSI (88 samples) and CEU (112 samples). For POPRES, partitioning on E₁ separated southern European population (1092 samples) and northern European population (1374 samples).