Skip to main content
. 2017 Nov 7;49:82. doi: 10.1186/s12711-017-0356-8

Table 2.

The 10 most significant SNPs associated with each calving performance trait at the genome-wise false discovery rate of 5%

Traita RefSNP (rs)b c Pos. (bp) MAF Estimated effect SE P-value Locationd Gene name
CA rs109478645 18 57589121 0.12 − 5.55 0.39 3.69E−41 5484 L LOC100138951
CA rs136283363 18 57548213 0.12 5.55 0.39 3.69E−41 5497L LOC615876
CA rs110801791 18 57516245 0.13 − 4.86 0.38 4.51E−35 1252 R CTU1
CA rs135253383 18 57520290 0.13 4.83 0.38 1.27E−34 Within CTU1
CA rs136514789 18 57486184 0.16 3.92 0.34 1.50E−28 1330 L LOC540297
CA rs109882115 18 58067310 0.28 − 3.15 0.29 1.71E−25 Within ENSBTAG00000039491
CA rs132734257 18 57511637 0.19 − 3.54 0.33 2.04E−25 5860 R CTU1
CA rs135508298 18 59602905 0.21 3.52 0.33 2.12E−25 75902 L ENSBTAG00000048191
CA rs134539659 18 59612379 0.21 − 3.52 0.33 2.12E−25
CA rs109540436 18 59890631 0.20 3.37 0.33 2.98E−23 3982 R LOC100300095
CEc rs110801791 18 57516245 0.13 − 3.93 0.49 2.72E−15 1252 R CTU1
CEc rs135253383 18 57520290 0.13 3.90 0.49 4.08E−15 Within CTU1
CEc rs109478645 18 57589121 0.12 − 3.86 0.51 7.21E−14 5484 L LOC100138951
CEc rs136283363 18 57548213 0.12 3.86 0.51 7.21E−14 5497L LOC615876
CEc rs137554975 18 56944300 0.15 − 2.98 0.45 4.04E−11 Within MYH14
CEc rs136113894 18 56959011 0.16 − 2.82 0.44 2.25E−10 Within KCNC3
CEc rs136514789 18 57486184 0.16 2.79 0.44 5.19E−10 1330 L LOC540297
CEc rs133544315 18 60019327 0.21 2.61 0.42 7.62E−10 47852 L ZNF836
CEc rs109540436 18 59890631 0.20 2.45 0.42 9.69E−09 3982 R LOC100300095
CEc rs135033267 18 60043680 0.20 − 2.45 0.43 1.13E−08 25523 R ENSBTAG00000011844
CEh rs110801791 18 57516245 0.13 − 3.73 0.46 1.33E−15 1252 R CTU1
CEh rs135253383 18 57520290 0.13 3.69 0.46 2.77E−15 Within CTU1
CEh rs109478645 18 57589121 0.12 − 3.73 0.48 1.92E−14 5484 L LOC100138951
CEh rs136283363 18 57548213 0.12 3.73 0.48 1.92E−14 5497L LOC615876
CEh rs133544315 18 60019327 0.21 2.45 0.40 9.84E−10 47852 L ZNF836
CEh rs109540436 18 59890631 0.20 2.41 0.40 2.17E−09 3982 R LOC100300095
CEh rs135033267 18 60043680 0.20 − 2.41 0.40 2.69E−09 25523 R ENSBTAG00000011844
CEh rs137436636 18 60006650 0.20 2.41 0.40 2.69E−09 35175 L ZNF836
CEh rs136514789 18 57486184 0.16 2.49 0.42 3.36E−09 1330 L LOC540297
CEh rs133144614 18 59242260 0.41 − 1.99 0.34 4.68E−09 13197 L ZNF845
CSh rs43264905 1 118222449 0.04 4.91 0.85 9.51E−09 15187 L ENSBTAG00000038069
DCA rs110801791 18 57516245 0.13 − 4.27 0.57 1.26E−13 1252 R CTU1
DCA rs135253383 18 57520290 0.13 4.23 0.57 2.06E−13 Within CTU1
DCA rs109478645 18 57589121 0.12 − 4.25 0.59 1.59E−12 5484 L LOC100138951
DCA rs136283363 18 57548213 0.12 4.25 0.59 1.59E−12 5497L LOC615876
DCA rs136514789 18 57486184 0.16 3.18 0.51 8.24E−10 1330 L LOC540297
DCA rs41601357 18 58800104 0.49 2.33 0.40 5.86E−09 7804 L LOC101904049
DCA rs133144614 18 59242260 0.41 − 2.41 0.42 8.66E−09 13197 L ZNF845
DCA rs109011289 18 59058582 0.48 − 2.27 0.40 1.99E−08 7587 L LOC101904371
DCA rs41582522 18 58666276 0.41 − 2.33 0.41 2.47E−08
DCA rs133544315 18 60019327 0.21 2.76 0.49 2.55E−08 47852 L ZNF836
SCEc rs109478645 18 57589121 0.12 − 6.19 0.40 1.07E−47 5484 L LOC100138951
SCEc rs136283363 18 57548213 0.12 6.19 0.40 1.07E−47 5497L LOC615876
SCEc rs110801791 18 57516245 0.13 − 5.66 0.39 1.36E−43 1252 R CTU1
SCEc rs135253383 18 57520290 0.13 5.65 0.39 1.66E−43 Within CTU1
SCEc rs136514789 18 57486184 0.16 4.38 0.36 1.81E−32 1330 L LOC540297
SCEc rs132734257 18 57511637 0.19 − 4.05 0.34 1.21E−30 5860 R CTU1
SCEc rs137554975 18 56944300 0.15 − 4.21 0.35 1.42E−30 Within MYH14
SCEc rs136113894 18 56959011 0.16 − 4.07 0.35 3.22E−29 Within KCNC3
SCEc rs135508298 18 59602905 0.21 3.90 0.34 7.48E−29 75902 L ENSBTAG00000048191
SCEc rs134539659 18 59612379 0.21 − 3.90 0.34 7.48E−29
SCEh rs109478645 18 57589121 0.12 − 6.13 0.46 4.12E−37 5484 L LOC100138951
SCEh rs136283363 18 57548213 0.12 6.13 0.46 4.12E−37 5497L LOC615876
SCEh rs110801791 18 57516245 0.13 − 5.42 0.44 4.98E−32 1252 R CTU1
SCEh rs135253383 18 57520290 0.13 5.38 0.44 1.17E−31 Within CTU1
SCEh rs136514789 18 57486184 0.16 4.39 0.40 3.24E−26 1330 L LOC540297
SCEh rs132734257 18 57511637 0.19 − 4.03 0.39 2.30E−24 5860 R CTU1
SCEh rs109882115 18 58067310 0.28 − 3.53 0.34 1.33E−23 Within ENSBTAG00000039491
SCEh rs135508298 18 59602905 0.21 3.90 0.39 5.03E−23 75902 L ENSBTAG00000048191
SCEh rs134539659 18 59612379 0.21 − 3.90 0.39 5.03E−23
SCEh rs43038601 18 57491196 0.22 − 3.59 0.36 4.60E−22 4128 R KLK14
SCSc rs109478645 18 57589121 0.12 − 5.59 0.82 1.50E−11 5484 L LOC100138951
SCSc rs136283363 18 57548213 0.12 5.59 0.82 1.50E−11 5497L LOC615876
SCSc rs136113894 18 56959011 0.16 − 4.41 0.71 9.17E−10 Within KCNC3
SCSc rs110801791 18 57516245 0.13 − 4.73 0.79 3.63E−09 1252 R CTU1
SCSc rs135253383 18 57520290 0.13 4.73 0.79 3.63E−09 Within CTU1
SCSc rs134066287 18 62844651 0.23 3.84 0.65 3.70E−09 Within FCAR
SCSc rs109882115 18 58067310 0.28 − 3.56 0.60 3.96E−09 Within ENSBTAG00000039491
SCSc rs109844326 18 63415091 0.16 4.19 0.72 9.77E−09 2950 L MBOAT7
SCSc rs134353106 18 62839617 0.26 3.47 0.61 2.13E−08 5900 L KIR2DL5A
SCSc rs133544315 18 60019327 0.21 3.74 0.67 2.82E−08 47852 L ZNF836
SCSh rs109478645 18 57589121 0.12 − 7.95 0.86 1.86E−19 5484 L LOC100138951
SCSh rs136283363 18 57548213 0.12 7.95 0.86 1.86E−19 5497L LOC615876
SCSh rs133544315 18 60019327 0.21 5.91 0.71 1.97E−16 47852 L ZNF836
SCSh rs110801791 18 57516245 0.13 − 6.94 0.83 2.84E−16 1252 R CTU1
SCSh rs135253383 18 57520290 0.13 6.86 0.83 5.87E−16 Within CTU1
SCSh rs109540436 18 59890631 0.20 5.76 0.71 1.05E−15 3982 R LOC100300095
SCSh rs135033267 18 60043680 0.20 − 5.72 0.71 1.98E−15 25523 R ENSBTAG00000011844
SCSh rs137436636 18 60006650 0.20 5.72 0.71 1.98E−15 35175 L ZNF836
SCSh rs136514789 18 57486184 0.16 6.02 0.75 3.07E−15 1330 L LOC540297
SCSh rs136766893 18 58494682 0.26 − 5.02 0.63 6.02E−15 Within BOSTAUV1R416

aTraits = evaluated calving traits included calving ability (CA), daughter calving ability (DCA), maternal calving ease at first calving (heifer; CEh), maternal calf survival at first calving (heifer; CSh), maternal calving ease at later calvings (cow; CEc), maternal calf survival at later calvings (cow; CSc), direct calving ease at first calving (heifer; SCEh), direct calf survival at first calving (heifer; SCSh), direct calving ease at later calvings (cow; SCEc), direct calf survival at later calvings (cow; SCSc) and sire conception rate (SCR). Calving performance traits are expressed as relative breeding values with a population average of 100 and standard deviation of 5

bRefSNP (rs) = assigned reference SNP (rs) number for a SNP by the National Center for Biotechnology Information

cBTA = Bos taurus autosomes

dLocation = gene location (within L left or R right) from the SNP of interest