Table 2.
Top five genes based on gene-based association statistics for resistance to clinical mastitis
| Lead SNP | Top 5 Genes* | Gene P value |
|---|---|---|
| 3:92927352 | PLPP3, TXNDC12, RAB3B, NRDC, ENSBTAG00000046915 | 1.46e-08 |
| 4:10928348 | ASB4, ANKIB, COL28A1, DYNC1I1, PON1 | 1.83e-06 |
| 4:58490979 | TBX20, IMMP2L, ST7, LAMB4, ELMO1 | 9.77e-09 |
| 5:30211323 | SLC2A13, SLC38A1, RPAP3, TMEM117, LIMA1 | 6.80e-10 |
| 5:106360448 | CCDC77, LOC100336690,ABCC9,KDM5A, FGF6 | 1.56e-08 |
| 6:23469606 | TBCK, TSPAN5, PPA2, PPP3CA, NFKB1 | 1.33e-09 |
| 6:87299659 | NPFFR2, SULT1E1, SLC4A4, DCK, LOC100140490 | 2.50e-26 |
| 6: 93131207 | PARM1, SHROOM3, MTHFD2L, SEPT11, EPGN | 2.16e-14 |
| 7:31253987 | C3, PCDHB11, PCDHB6, FBN3, LOC786512 | 1.27e-08 |
| 8:25684799 | ADAMTSL1, MLLT3, PLPPR1, MTAP, FOCAD | 3.15e-08 |
| 9:80007099 | ESR1, RAET1G, PPP1R14C, SYNE1, SHPRH | 4.16e-07 |
| 10:51191670 | RORA, MYO1E, RNF111, DUOX1,SLC28A2 | 2.93e-08 |
| 11:88742878 | PDIA6, ATP6V1C2, CAPG, TBC1D8, MGAT4A | 4.43e-08 |
| 13:62017506 | BMP7, TFAP2C, NSFL1C, NDRG3, REM1 | 2.01e-14 |
| 14:61344981 | DPYS, KCNQ3, TPD52, RSPO2, PARP10 | 1.44e-07 |
| 16:47836093 | SMYD3, ACOT7, MEGF6, ENSBTAG00000019339, CHD5 | 8.28e-13 |
| 18:43909571 | HPN, GPI, WTIP, PDCD2L, TGFB1 | 7.08e-09 |
| 19:43038655 | SP2, TBCD, OSBPL7, SRCIN1, CBX1 | 2.22e-13 |
| 20:38471456 | PLCXD3, WDR70, RICTOR, MROH2B, NUP155 | 2.99e-14 |
| 23:11477905 | ZFAND3, CPNE5, DNAH8, KCTD20, PPARD | 1.05e-11 |
| 25:35354412 | TMEM130, CORO7, VASN, CDIP1, DNAJA3 | 2.09e-08 |
| 26:20463679 | PDE6C, BTRC, SEMA4G, CNNM2, SLK | 7.43e-09 |
*Top five genes selected based on the ranking of P value, if the –log10 (P) > 5.60, the genes are listed in the table
# The P value listed in the table is for the gene with highest P value among the top five genes showing association. The model to calculate the gene P value in MAGMA [17] was snp-wise = mean