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Table 1 SNPs included in the SNPlex genotyping panel

From: Single nucleotide polymorphisms in candidate genes associated with milk yield in Argentinean Holstein and Holstein x Jersey cows

Candidate gene Marker Location (BTA:bp) Call rate MAF HWE
p-value
ARL4A rs43375517 4:20296999 98.1 0.39 0.14
ETV1 rs42213673 4:22111819 98.8 0.35 0.28
SNX13 rs41595314 4:26425057 98.6 0.07 8.10− 3
LEP rs29004488 4:93262056 97.4 0.33 0.02
OLR1 rs109019599 5:100254823 89.3 0.25 2.10−3
ABCG2 rs43702337 6:38027010 99.7 0.00 1.00
OPN rs132812135 6:38120968 94.5 0.35 0.55
rs110930453 6:38122665 93.1 0.42 0.87
OPN3907a 6:38128806    
PPARGC1A rs109579682 6:44875251 98.4 0.23 0.03
rs133669403 6:44875315 97.5 0.08 0.09
rs17870811 6:44875421 99.5 0.06 0.46
CSN1S1 CSN1_AB 6:87146017 87.9 0.00 1.00
rs433385179 6:87148464 99.9 0.00 1.00
rs43703010 6:87157262 96.8 0.15 0.64
CSN2 rs43703013 6:87181453 96.8 0.04 0.02
rs43703011 6:87181619 97.6 0.27 0.01
CSN3 rs43706475 6:87390479 99.3 0.00 1.00
rs43703015 6:87390576 99.4 0.19 0.33
rs43703017 6:87390632 98.2 0.04 0.33
LGB rs41255680 11:103301242    
rs41255685 11:103301690 75.3 0.08 < 1.10−6
rs43691049 11:103303343    
rs109625649 11:103304757 83.5 0.10 0.56
DGAT1 rs109234250 14:1802265 62.8 0.10 0.61
rs109326954 14:1802266 62.8 0.10 0.61
STAT5A rs109487069 19:43047829    
GH rs109191047 19:48768766 97.5 0.19 0.19
rs137651874 19:48769040 98.1 0.48 0.10
FASN rs208645216 19:51400139    
rs41919985 19:51402032 78.7 0.15 2.10−3
GHR rs385640152 20:31909478 98.8 0.09 0.84
PRLR rs135164815 20:39115344 99.2 0.15 0.91
UTMP rs132991801 21:59667572 96.0 0.42 0.03
LTF rs41256920 22:53521978 99.2 0.23 0.39
rs43706485 22:53522038 95.5 0.19 0.93
PRL rs211032652 23:35106206 99.5 0.08 0.57
rs110494133 23:35110974 97.4 0.21 3.10−6
SCD1 rs41255693 26:21144708 98.9 0.19 0.17
  1. aOPN3907 is a T deletion, not a SNP
  2. Call rate, MAF and HWE p-value for the SNPs that did not present failure in the genotyping reactions are indicated. Markers bolded in black passed the quality control checks. Location of the SNPs is based on assembly UMD3.1