Table 2. Inbreeding coefficient and mean heterozygosity in NL, BBC, IRE, CEU and TSI populations.

Pop	SNPs useda	Number of SNPs	Ho	He	F
NL	Common	174 754	0.3411	0.3428	0.005±0.037
IRE	Common	174 754	0.3419	0.3415	−0.001±0.07
BBC	Common	174 754	0.3425	0.3428	0.001±0.02
CEU	Common	174 754	0.3445	0.3429	−0.005±0.006
TSI	Common	174 754	0.3434	0.3417	−0.005±0.005
NL	Pruned	567 352	0.2258	0.2265	0.003±0.037
IRE	Pruned	237 709	0.3164	0.3155	−0.003±0.07
BBC	Pruned	366 800	0.2389	0.2391	0.001±0.02
CEU	Pruned	338 262	0.2783	0.2757	−0.009±0.006
TSI	Pruned	341 622	0.2810	0.2779	−0.011±0.005
NL	All	1 198 360	0.2576	0.2588	0.005±0.037
IRE	All	545 176	0.3305	0.3304	−0.000±0.07
BBC	All	1 026 111	0.2938	0.2940	0.001±0.02
CEU	All	1 388 221	0.3148	0.3133	−0.005±0.006
TSI	All	1 389 386	0.3151	0.3135	−0.005±0.005

H_o: mean observed population heterozygosity rate; H_e: mean expected population heterozygosity rate from the Hardy–Weinberg equation.

F: mean population inbreeding coefficient, calculated as F=(H_e−H_o)/H_e. The mean SNP heterozygosity rate for each individual was calculated using Haploview. The mean heterozygosity rate was then calculated for each population.

^aCommon: SNPs were found in all five populations; Pruned: those SNPs remaining when SNPs in high LD with an adjacent SNP (r²>0.5) were removed.