Table 1. Top 20 genomic regions identified as selection candidates in MKK using the Fst statistic and clustering.
Chr | Start location | Stop location | Genes in region | Number of HighFst SNPs (empiricalp-value <0.001) | Max Fst within cluster | Max XP-EHH score within cluster |
2 | 135036696 | 136726567 | RAB3GAP1, ZRANB3, DARS, R3HDM1, TMEM163,YSK4, LCT, UBXN4, MCM6, MGAT5, CCNT2 | 123 | 0.382 | 12.202 |
2 | 78305622 | 78500655 | - | 33 | 0.311 | 3.805 |
12 | 56402204 | 56754137 | PAN2, OBFC2B, SLC39A5, APOF, STAT2, CS,RNF41, IKZF4, SMARCC2 | 28 | 0.283 | 3.024 |
3 | 191929784 | 191990575 | FGF12 | 13 | 0.272 | 5.222 |
5 | 115126388 | 115223035 | ATG12, AP3S1 | 7 | 0.266 | 3.870 |
2 | 163048404 | 163152351 | IFIH1, FAP | 19 | 0.261 | 3.108 |
7 | 99053816 | 99436198 | ZNF498, CYP3A4, CPSF4, CYP3A7, CYP3A43 | 17 | 0.260 | 3.290 |
1 | 12296232 | 12319994 | VPS13D | 4 | 0.253 | 3.060 |
22 | 49978502 | 50077531 | - | 4 | 0.244 | 3.732 |
5 | 32128179 | 32159329 | GOLPH3 | 5 | 0.242 | 3.062 |
5 | 14747247 | 14750823 | ANKH | 4 | 0.237 | 6.800 |
14 | 36033703 | 36201722 | RALGAPA1 | 4 | 0.221 | 3.517 |
2 | 136917330 | 136921703 | - | 2 | 0.218 | 8.549 |
1 | 198692364 | 198745866 | PTPRC | 2 | 0.212 | 3.138 |
2 | 137580234 | 137595545 | - | 4 | 0.209 | 4.871 |
12 | 111414527 | 111502280 | CUX2 | 5 | 0.209 | 3.393 |
17 | 75423198 | 75431978 | SEPT9 | 3 | 0.200 | 5.024 |
18 | 66714832 | 66724690 | CCDC102B | 4 | 0.200 | 5.704 |
1 | 74807337 | 74842787 | TNNI3K | 3 | 0.193 | 3.993 |
3 | 185752767 | 185805993 | ETV5 | 3 | 0.192 | 4.569 |
1,232 SNPs with significant Fst scores (pB<8.6E−6, pE<0.001) were clustered into contiguous genomic regions of linkage disequilibrium. A cluster was defined as a collection of SNPs in a genomic region where each SNP had genotype R2≥0.25 with at least one other SNP in the cluster. Clusters containing a SNP with maximum XP-EHH score >3 were identified as being MKK associated. The 22 top clusters are ranked by the highest Fst value for a SNP pair in a cluster. The complete set of clusters identified by Fst is in Table S2.