Table 3 List of the top 10 |iHS| and positive XP-EHH for the SNP markers in GH100 and GJ, and their closest genes, with information on the Bos taurus chromosome (BTA) position
From: Genomic analysis reveals population structure and selection signatures in plateau dairy cattle
Test | SNP | BTA | Position | |iHS|/XP-EHH | Annotated genes |
|---|---|---|---|---|---|
iHS (GH100) | BovineHD0900030245 | 9 | 101,767,952 | 4.48 | RPS6KA2,RNASET2,CEP43,CCR6,GPR31 |
iHS (GH100) | BovineHD0500030656 | 5 | 106,261,952 | 4.45 | PARP11,CRACR2A,PRMT8 |
iHS (GH100) | BovineHD0300000421 | 3 | 1,581,101 | 4.10 | POU2F1,STYXL2,GPA33 |
iHS (GH100) | ARS-BFGL-NGS-66811 | 27 | 12,414,458 | 3.97 | N.A |
iHS (GH100) | ARS-BFGL-NGS-102044 | 9 | 102,110,374 | 3.96 | CCR6,GPR31,TTLL2,UNC93A,AFDN |
iHS (GH100) | Hapmap35530-SCAFFOLD65737_1657 | 22 | 36,411,261 | 3.95 | N.A |
iHS (GH100) | BTA-67311-no-rs | 3 | 1,531,782 | 3.91 | POU2F1,STYXL2,GPA33 |
iHS (GH100) | BovineHD0300000445 | 3 | 1,645,135 | 3.91 | POU2F1,STYXL2,GPA33,MAEL |
iHS (GH100) | BovineHD3000044205 | 30 | 137,652,192 | 3.84 | N.A |
iHS (GH100) | ARS-BFGL-NGS-91848 | 6 | 18,195,932 | 3.79 | DKK2 |
XP-EHH (GH100) | BovineHD0400007618 | 4 | 26,173,337 | 3.68 | SNX13 |
XP-EHH (GH100) | ARS-BFGL-NGS-38856 | 20 | 5,397,009 | 3.55 | BOD1 |
XP-EHH (GH100) | BTB-01383912 | 4 | 26,109,668 | 3.54 | N.A |
XP-EHH (GH100) | Hapmap31211-BTA-29377 | 7 | 68,574,155 | 3.51 | N.A |
XP-EHH (GH100) | BovineHD2000001656 | 20 | 5,392,046 | 3.49 | BOD1 |
XP-EHH (GH100) | BovineHD0400029309 | 4 | 103,308,051 | 3.42 | HIPK2,TBXAS1,PARP12 |
XP-EHH (GH100) | BovineHD0200038391 | 2 | 131,340,253 | 3.32 | RAP1GAP,ALPL,ECE1,EIF4G3 |
XP-EHH (GH100) | BovineHD0600010456 | 6 | 36,395,590 | 3.29 | HERC3,PYURF,HERC5,HERC6,PPM1K,ABCG2 |
iHS (GJ) | BovineHD0100035549 | 1 | 125,040,443 | 5.67 | DIPK2A,SLC9A9 |
iHS (GJ) | BovineHD0200007620 | 2 | 26,291,885 | 5.38 | MYO3B,UBR3 |
iHS (GJ) | BovineHD1800009949 | 18 | 32,766,212 | 5.05 | CDH11 |
iHS (GJ) | BovineHD0900026973 | 9 | 93,742,851 | 5.04 | ARID1B,TMEM242 |
iHS (GJ) | BovineHD0900026974 | 9 | 93,744,138 | 5.04 | ARID1B,TMEM242 |
iHS (GJ) | BPI-2 | 13 | 67,172,651 | 5.03 | TGM2,KIAA1755,BPI,LBP |
iHS (GJ) | BovineHD1100022373 | 11 | 77,869,084 | 4.61 | TDRD15,APOB |
iHS (GJ) | BovineHD1500020381 | 15 | 69,760,189 | 4.50 | N.A |
iHS (GJ) | BovineHD2200007996 | 22 | 27,616,751 | 4.46 | CNTN3 |
iHS (GJ) | ARS-BFGL-NGS-68739 | 8 | 5,147,600 | 4.23 | N.A |
XP-EHH (GJ) | BovineHD0800009655 | 8 | 31,812,018 | 4.16 | TYRP1 |
XP-EHH (GJ) | Hapmap54720-rs29023017 | 8 | 31,818,769 | 4.02 | TYRP1 |
XP-EHH (GJ) | BovineHD0800009650 | 8 | 31,796,418 | 3.99 | TYRP1 |
XP-EHH (GJ) | ARS-BFGL-NGS-23687 | 23 | 8,154,656 | 3.89 | GRM4,HMGA1,SMIM29,NUDT3 |
XP-EHH (GJ) | BTA-123382-no-rs | 8 | 31,779,503 | 3.87 | TYRP1 |
XP-EHH (GJ) | BovineHD0800009630 | 8 | 31,751,207 | 3.76 | LURAP1L,TYRP1 |
XP-EHH (GJ) | BovineHD1600002717 | 16 | 9,494,040 | 3.73 | N.A |
XP-EHH (GJ) | BTA-81018-no-rs | 8 | 31,845,307 | 3.72 | TYRP1 |
XP-EHH (GJ) | BovineHD0800009641 | 8 | 31,850,020 | 3.68 | N.A |
XP-EHH (GJ) | Hapmap43060-BTA-81019 | 8 | 31,867,242 | 3.65 | N.A |