Table 3. Regions identified across the genome by different discovery mechanisms using the three bioinformatic metrics calculated from the CHB and CHS genome-wide data from HapMap and SGVP.
| Discovery mechanism | Chr | Start (Mb) | End (Mb) | FSTa (window size) | XP-EHHb (direction) | iHS (CHB) | iHS (CHS) | MAF latitude correlation Pc (rsID) | SNP loadings (rsID) | Genes |
|---|---|---|---|---|---|---|---|---|---|---|
| iHS | 3 | 189.512 | 190.012 | No evidence | Top 0.5% (positive) | Top 0.01% | No evidence | 2.5 × 10−3 (rs16863396) | Top 0.5% (rs3817462) | LPP |
| FST, iHS | 4 | 100.552 | 101.052 | Top 0.1% (100 kb, 500 kb) | Top 0.5% (positive) | Top 0.1% | No evidence | 7.7 × 10−3 (rs13150247) | Top 0.1% (rs13150247) | ADH gene cluster, RG9MTD2, MTTP, DAPP1, MAP2K1IP1, DNAJB14 |
| iHS | 6 | 18.610 | 19.110 | No evidence | Top 0.1% (positive) | Top 0.1% | No evidence | 9.5 × 10−4 (rs986148) | No evidence | NA |
| FST, XP-EHH | 6 | 29.795 | 29.895 | Top 0.01% (100 kb, 500 kb) | Top 0.01% (negative) | No evidence | No evidence | 1.3 × 10−2 (rs1633021) | Top 0.1% (rs3131020) | HLA-F, HLA-G |
| FST | 11 | 61.189 | 61.689 | Top 0.1% (100 kb, 500 kb) | Top 0.1% (positive) | Top 0.5% | No evidence | No evidence | Top 0.5% (rs1495941) | FEN1, FADS1-3, RAB3IL1, BEST1, FTH1, INCENP |
| XP-EHH | 12 | 71.358 | 73.069 | Top 0.01% (100 kb) | Top 0.01% (negative) | No evidence | Top 0.5% | 8.6 × 10−3 (rs2102755) | Top 0.5% (rs10879537) | NA |
| FST, XP-EHH | 13 | 97.957 | 98.957 | Top 0.1% (100 kb, 500 kb) | Top 0.01% (negative) | No evidence | Top 0.5% | 9.1 × 10−2 (rs11069349) | No evidence | STK24, SLC15A1, DOCK9, PHGDHL1, GPR18, EBI2 |
Abbreviations: CHB, Han Chinese from Beijing; CHS, Singapore Chinese with South China ancestries; HGDP, Human Genome Variation Project; iHS, integrated haplotype score; SGVP, Singapore Genome Variation Project; XP-EHH, cross-population extended haplotype homozygosity.
Regional evidence from the FST metric, where the size of the region containing evidence is defined in the parentheses.
XP-EHH between CHB and CHS, with positive indicating evidence of positive selection in CHB, whereas negative indicating evidence of positive selection in CHS.
Bonferroni corrected P-value for the test of correlation between allele frequencies and latitude of the 22 East and South-East Asian populations from HapMap, HGDP and SGVP. The Bonferroni correction is performed by multiplying the empirical P-value by the number of SNPs found in each region.
These metrics utilizing the discovery populations of CHB and CHS are described in Table 1.