Family- and population-based designs identify different rare causal variants

BMC Proceedings

Table 1 Two-point linkage analysis using family-based data

Gene	SNP with highest β		SNP with highest MAF		Number of simulation
	SNP	β	SNP	MAF	LOD ≥ 1 (α = 10⁻²)	LOD ≥ 2 (α = 10⁻³)	LOD ≥ 3 (α = 10⁻⁴)	LOD ≥ 4 (α = 10⁻⁵)
ARNT	C1S6561	0.65721	C1S6533	0.011478	1	0	0	0
ELAVL4	C1S3181	0.76911	C1S3181	0.000717	3	0	0	0
			C1S3182	0.000717
FLT1	C13S479	0.75946	C13S523	0.066714	4	0	0	0
FLT4	C5S5156	0.43010	C5S5133	0.001435	10	1	0	0
HIF1A	C14S1729	0.28532	C14S1734	0.012195	1	0	0	0
HIF3A	C19S4831	0.29287	C19S4799	0.000717	43	3	0	0
			C19S4815	0.000717
			C19S4831	0.000717
KDR	C4S1877	1.07706	C4S1878	0.164993	48	9	0	0
VEGFA	C6S2981	1.20645	C6S2981	0.002152	198	172	110	55
VEGFC	C4S4935	1.35726	C4S4935	0.000717	197	167	126	76

ISSN: 1753-6561