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. 2017 Jan 18;34(3):559–574. doi: 10.1093/molbev/msw249

Table 6.

Locus-Specific Fst and Allele Frequencies within the 1000 Genomes Populations for the Five Most Differentiated SNPs in Distinct Genome Regions in the Brazil Amerindian Component vs. Closest Asian Population (BEB)

Populationa LWK TSI BEB PJL CHB JPT CHS GIH KHV CDX BRN
Nb 97 107 86 96 103 104 105 101 99 93 1538
SNP CHR:POS A1 A2 Fst LWKc Fst TSIc Fst BEBc Fst PJLc Fst CHBc Fst JPTc Fst CHSc Fst GIHc Fst KHVc Fst CDXc
rs7631391 3:64514393 G A 0.858 0.950 0.885 0.909 0.634 0.685 0.682 0.889 0.671 0.694
rs77594147 5:169155975 G A 0.240 0.826 0.857 0.801 0.782 0.777 0.795 0.817 0.822 0.785
rs28649017 15:85438991 A G 0.102 0.242 0.827 0.843 −0.003 0.024 0.052 −0.001 0.008 −0.003
rs7151991 14:32635572 A G 0.813 0.754 0.821 0.749 0.794 0.791 0.766 0.677 0.749 0.707
rs45601437 16:10989754 A G 0.827 0.901 0.816 0.820 0.511 0.586 0.567 0.865 0.628 0.629
SNP CHR:POS A1 A2 f(A1) LWKd f(A1) TSId f(A1) BEBd f(A1) PJLd f(A1) CHBd f(A1) JPTd f(A1) CHSd f(A1) GIHd f(A1) KHVd f(A1) CDXd f(A1) BRN2Amrd
rs7631391 3:64514393 G A 0.082 0.000 0.058 0.036 0.286 0.240 0.243 0.054 0.253 0.231 0.950
rs77594147 5:169155975 G A 0.541 0.042 0.017 0.063 0.078 0.082 0.067 0.050 0.045 0.075 0.878
rs28649017 15:85438991 A G 0.356 0.500 0.983 0.995 0.141 0.245 0.291 0.173 0.101 0.145 0.150
rs7151991 14:32635572 A G 0.124 0.178 0.116 0.182 0.141 0.144 0.167 0.248 0.182 0.220 0.950
rs45601437 16:10989754 A G 0.072 0.009 0.081 0.078 0.345 0.279 0.295 0.040 0.242 0.242 0.912
a

The populations are ordered by Africa(LWK), Europe(TSI), Asia(BEB, PJL, CHB, JPT, CHS, GIH, KHV, and CDX) where Asian populations are in decreasing order of similarity to BRN2(Amr) (supplementary table S5, Supplementary Material online). Population codes are LWK (Luhya in Webuye, Kenya); TSI (Toscani in Italy); BEB (Bengalis in Bangladesh); PJL (Punjabis in Lahore, Pakistan); CHB (Han Chinese in Beijing); JPT (Japanese in Tokyo, Japan); CHS (Southern Han Chinese); GIH (Gujarati in Houston, USA); KHV (Kinh in Ho Chi Minh City, Vietnam); CDX (Chinese Dai in Xishuangbanna); BRN2(Amr) (North-Eastern Brazilians, Amerindian admixture component 2).

b

Number of DNA samples within each population.

c

SNP-specific Fst value for each population compared with the Brazil Amerindian admixture component, BRN2 (Amr). In the top half of the table, the BEB Fst values are shown in bold since this is the closest Asian population and are the values in table 5. In the lower half of the table, the BEB and BRN2(Amr) columns are in bold since the difference in these frequencies is used in the FstBEB calculation. Other Fst 1KG values in the top half of the table are calculated from the 1KG population and BRN2(Amr) frequencies in the lower half.

d

Frequency of the A1 allele in each population.