Table 2. Top 1 candidate genes identified among 36 pairs of Asian populations.
| Group Pair | Gene | Chromosome | No.SNPs | Top SNP | Alleles | Max FST | GO Function |
| SCT1_SCT2 | GALNTL6 | 4 | 10 | rs6811723 | T/C | 0.265 | O-Glycan biosynthesis, carbohydrate metabolism, protein metabolism and modification, smoking cessation. |
| SCT1_IND | TTLL11 | 9 | 1 | rs10513414 | T/C | 0.738 | Ligase activity, cell projection. |
| SCT1_INDO | AMZ1 | 7 | 3 | rs798527 | T/C | 0.578 | Proteolysis. |
| SCT1_MN | AMZ1 | 7 | 3 | rs798525 | A/C | 0.584 | Proteolysis. |
| SCT1_PN | FOXQ1 | 6 | 1 | rs951318 | A/G | 0.976 | Hair follicle development/morphogenesis, epidermis and ectoderm development. |
| SCT1_SEA | DAPP1 | 4 | 1 | rs10516445 | C/G | 0.464 | Phosphorus metabolic process. |
| SCT2_IND | MLKL | 16 | 4 | rs4888473 | G/A | 0.633 | Protein phosphorylation and modification. |
| SCT2_INDO | MTTP | 4 | 3 | rs2851292 | G/T | 0.461 | Lipid and protein transport, serum cholesterol level. |
| SCT2_MN | PPP1CC | 12 | 1 | rs11066232 | C/T | 0.492 | Cell division, metabolic processes of glycogen, phosphorus and hexose. |
| SCT2_PN | FOXQ1 | 6 | 1 | rs951318 | A/G | 0.977 | Hair follicle development/morphogenesis, epidermis and ectoderm development. |
| SCT2_SEA | MTTP | 4 | 3 | rs2851292 | G/T | 0.383 | Lipid and protein transport, serum cholesterol level. |
| Han_SCT1 | C1orf140 | 1 | 1 | rs851195 | T/C | 0.281 | / |
| Han_SCT2 | VEGFC | 4 | 6 | rs921879 | C/G | 0.223 | Angiogenesis, blood vessel development, regulation of amino acid phosphorylation and neuroblast proliferation, cell motion, cell surface receptor linked signal transduction, embryonic morphogenesis, epithelium development. |
| Han_IND | ABCA12 | 2 | 4 | rs1250233 | G/A | 0.728 | Lipid transport and localization, cellular homeostasis,. |
| Han_INDO | FMO6P | 1 | 4 | rs7527462 | C/G | 0.496 | / |
| Han_MN | BC035398 | 10 | 3 | rs1998643 | A/G | 0.532 | / |
| Han_PN | FOXQ1 | 6 | 1 | rs951318 | A/G | 0.977 | Hair follicle development/morphogenesis, epidermis and ectoderm development. |
| Han_SEA | DAPP1 | 4 | 1 | rs10516445 | C/G | 0.359 | Phosphorus metabolic process. |
| INDO_IND | TTLL11 | 9 | 2 | rs10513414 | T/C | 0.602 | Ligase activity, cell projection. |
| INDO_MN | AK096329 | 1 | 6 | rs477289 | A/C | 0.521 | / |
| INDO_PN | FOXQ1 | 6 | 2 | rs951318 | A/G | 0.977 | Hair follicle development/morphogenesis, epidermis and ectoderm development. |
| INDO_SEA | YTHDC2 | 5 | 2 | rs182988 | T/A | 0.323 | ATP binding, DNA/RNA helicase. |
| JK_SCT1 | A2BP1 | 16 | 40 | rs10500343 | C/T | 0.366 | RNA processing and localization. |
| JK_SCT2 | GRIP1 | 12 | 7 | rs7132697 | T/A | 0.276 | Protein localization, regulation of gene expression, steroid hormone receptor signaling pathway, androgen receptor signaling pathway, regulation of nitrogen compound metabolic process, regulation of RNA metabolic process. |
| JK_Han | DIAPH3 | 13 | 8 | rs300310 | T/C | 0.147 | Cytoskeleton organization. |
| JK_IND | ABCA12 | 2 | 4 | rs1250233 | G/A | 0.743 | Lipid transport and localization, cellular homeostasis |
| JK_INDO | MTTP | 4 | 3 | rs10516441 | G/A | 0.509 | Lipid and protein transport, serum cholesterol level. |
| JK_PN | FOXQ1 | 6 | 1 | rs951318 | A/G | 0.977 | Hair follicle development/morphogenesis, epidermis and ectoderm development. |
| JK_SEA | MTTP | 4 | 3 | rs10516441 | G/A | 0.449 | Lipid and protein transport, serum cholesterol level. |
| JK_MN | AX747662 | 1 | 7 | rs10489392 | A/G | 0.484 | / |
| MN_IND | CCDC104 | 2 | 3 | rs782603 | A/G | 0.69 | Membrane-enclosed lumen. |
| PN_IND | FOXQ1 | 6 | 2 | rs951318 | A/G | 0.897 | Hair follicle development/morphogenesis, epidermis and ectoderm development. |
| PN_MN | FOXQ1 | 6 | 1 | rs951318 | A/G | 0.979 | Hair follicle development/morphogenesis, epidermis and ectoderm development. |
| PN_SEA | FOXQ1 | 6 | 2 | rs951318 | A/G | 0.919 | Hair follicle development/morphogenesis, epidermis and ectoderm development. |
| SEA_IND | BX647987 | 4 | 1 | rs1230209 | T/G | 0.71 | / |
| SEA_MN | RGMB | 5 | 2 | rs1979980 | A/C | 0.48 | Cell adhesion, transmembrane receptor protein serine/threonine kinase signaling pathway, BMP signaling pathway, regulation of transcription and nitrogen compound metabolic process. |
Note: Groups are abbreviated as: JK – Japanese&Korean, Han – Han Chinese, SCT1 – SouthernChinese&Thai1, SCT2 – SouthernChinese&Thai2, INDO – Indonesian, PN – PhilippineNegrito, SEA – SoutheastAsian, MN – MalaysianNegrito, IND – Indian. Slash represents unknown gene function. After ranking candidates by averaging three SNPs that displayed higher FST within candidate genes, we put forward the top selection signal in each comparison of the nine groups, underlying the greatest possibility of population differentiation. No. SNP represents the number of SNPs within the gene. The function column shows the biological processes and phenotypic associations.