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Table 3 List of haplotypes in the Brown Swiss population identified by the trio-based approach

From: Mining massive genomic data of two Swiss Braunvieh cattle populations reveals six novel candidate variants that impair reproductive success

Name Chr Start End Allele frequency Proposed associated genea
BH1b 7 41371808 42545291 3.02 TCF3
BH2c 19 9726237 10819756 4.22 TUBD1
BH3 1 34908448 36034631 2.05  
BH4 1 76587512 77861430 2.20 GMNC
BH5 2 57787148 58768161 2.87 LRP1B
BH6 2 86065338 87460373 3.41 MARS2
BH7 2 120284002 121473182 1.93 SPATA3
BH8 2 127933873 129004898 2.98  
BH9 3 52432936 52,689742 1.43 HFM1
BH10 3 101636810 102827915 2.26  
BH11 4 108811998 109953666 2.66  
BH12 5 57653479 59777422 2.32 RNF41 and LRP1
BH13 5 110617654 111664596 1.63  
BH14 7 2588873 3357718 3.04 MRPL55
BH15 7 33954389 34956540 4.12  
BH16 7 79845977 80708046 2.20  
BH17 11 82034654 82881173 2.39 PGGHG
BH18 11 91766016 92804942 2.54  
BH19 11 103891372 105003404 1.77  
BH20 12 10254014 10967287 2.02  
BH21 12 74954939 75817277 1.61  
BH22 14 12290759 13350202 2.64  
BH23 17 69786512 70645226 2.98  
BH24 18 52977041 54113281 2.32 CPT1C
BH25 19 35808547 36844178 1.86 SNF8
BH26 19 47874708 48724082 1.89  
BH27 20 50058036 51370414 2.56  
BH28 21 19368258 20362870 1.60  
BH29 22 311724 1277064 2.07  
BH30 23 39600366 40609442 2.49  
BH31 25 27713801 29132187 1.80 ITGAD and SPN
BH32 26 9215188 10180467 1.72  
BH33 26 26659976 27689471 2.72  
BH34 26 31353340 32429589 2.37 ACSL5
BH35 27 28524504 29550764 1.80  
BH36 28 26661955 27743768 1.75  
BH37 28 45215132 45913154 2.07  
BH38 29 14497752 15554643 3.08  
  1. BH BS haplotype, Chr chromosome number, Start and End start and end positions according to the reference sequence ARS-UCD1.2 [36]
  2. aAccording to NCBI Annotation Release 106 [54]
  3. bPreviously described haplotype [19]
  4. ePreviously described haplotype and associated gene [11, 19]