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

Table 3.

The most highly significant SNPs associated with each body conformation trait at the genome-wise false discovery rate of 5%

Traita RefSNP (rs)b BTAc Pos. (bp) MAF Estimated effect SE P-value Locationd Gene name
ANG rs110434046 6 88919352 0.46829 − 2.46 0.40 1.35E−09
ANG rs137712965 6 88922396 0.46829 2.46 0.40 1.35E−09
ANG rs136287830 6 88865430 0.46168 − 2.43 0.40 2.21E−09
ANG rs108983037 6 88913092 0.46499 2.38 0.40 4.01E−09
ANG rs109512265 6 88485244 0.40611 − 2.19 0.38 1.51E−08 Within SLC4A4
BD rs109478645 18 57589121 0.1195 4.49 0.45 2.29E−22 Within ENSBTAG00000037537
BD rs136283363 18 57548213 0.1195 − 4.49 0.45 2.29E−22
BD rs110801791 18 57516245 0.12539 4.00 0.43 9.73E−20 1252 R CTU1
BD rs135253383 18 57520290 0.12549 − 3.99 0.43 1.03E−19 Within CTU1
BD rs132734257 18 57511637 0.19128 3.13 0.37 1.18E−16
BQ rs109901274 7 93244933 0.11506 − 2.81 0.43 9.10E−11 Within ARRDC3
BQ rs109618368 7 93254737 0.11506 2.81 0.43 9.10E−11 1643 L ARRDC3
BQ rs110680622 7 93287387 0.11506 − 2.81 0.43 9.10E−11
BQ rs110066813 7 93251138 0.13045 − 2.52 0.39 2.59E−10 Within ARRDC3
BQ rs109860522 7 93263102 0.13045 2.52 0.39 2.59E−10
CW rs109901274 7 93244933 0.11506 3.10 0.51 1.47E−09 Within ARRDC3
CW rs109618368 7 93254737 0.11506 − 3.10 0.51 1.47E−09 1643 L ARRDC3
CW rs110680622 7 93287387 0.11506 3.10 0.51 1.47E−09
CW rs110434046 6 88919352 0.46829 2.22 0.41 5.90E−08
CW rs137712965 6 88922396 0.46829 − 2.22 0.41 5.90E−08
DS rs109478645 18 57589121 0.1195 2.86 0.45 4.48E−10 Within ENSBTAG00000037537
DS rs136283363 18 57548213 0.1195 − 2.86 0.45 4.48E−10
DS rs136514789 18 57486184 0.15844 − 2.29 0.39 5.21E−09 1330 L LOC540297
DS rs110801791 18 57516245 0.12539 2.39 0.44 5.02E−08 1252 R CTU1
DS rs134321289 18 58053410 0.31698 − 1.73 0.32 5.49E−08
FA rs109517032 20 26955400 0.26761 2.31 0.40 1.11E−08
FA rs110521341 20 26957866 0.26761 − 2.31 0.40 1.11E−08
FA rs109222733 20 26960799 0.26761 − 2.31 0.40 1.11E−08
FA rs109747498 20 26978980 0.26761 − 2.31 0.40 1.11E−08
FA rs110486797 20 26990879 0.26761 − 2.31 0.40 1.11E−08
FTP rs133797664 8 79527489 0.1322 2.55 0.49 2.73E−07
FTP rs136251125 18 42320881 0.29168 1.67 0.32 3.28E−07
FTP rs136974352 18 42322043 0.29168 1.67 0.32 3.28E−07
FTP rs43571286 8 79497558 0.13468 2.42 0.47 3.66E−07
FTP rs137127919 5 12712534 0.06083 2.71 0.53 3.84E−07
PS rs42244554 5 1278211 0.3427 2.00 0.36 2.35E−08 694 L ZFC3H1
PW rs137169221 13 4626355 0.11558 − 2.73 0.46 5.63E−09
PW rs109478645 18 57589121 0.1195 2.53 0.43 6.48E−09 Within ENSBTAG00000037537
PW rs136283363 18 57548213 0.1195 − 2.53 0.43 6.48E−09
PW rs42382059 13 4518102 0.1165 − 2.60 0.46 2.12E−08
PW rs42382046 13 4524429 0.1165 2.60 0.46 2.12E−08
RAH rs109901274 7 93244933 0.11506 − 3.10 0.49 2.88E−10 Within ARRDC3
RAH rs109618368 7 93254737 0.11506 3.10 0.49 2.88E−10 1643 L ARRDC3
RAH rs110680622 7 93287387 0.11506 − 3.10 0.49 2.88E−10
RAH rs109343241 18 59615343 0.27577 1.93 0.35 4.08E−08
RAH rs135508298 18 59602905 0.20564 2.12 0.39 9.37E−08
ST rs109882115 18 58067310 0.2799 1.86 0.30 1.19E−09 Within ENSBTAG00000039491
ST rs109478645 18 57589121 0.1195 2.53 0.41 1.22E−09 Within ENSBTAG00000037537
ST rs136283363 18 57548213 0.1195 − 2.53 0.41 1.22E−09
ST rs133960300 5 106250561 0.14439 − 2.34 0.39 2.94E−09 3346 R CCND2
ST rs109685956 5 106256616 0.14439 − 2.34 0.39 2.94E−09 Within CCND2
TL rs110895486 5 12438670 0.21287 3.00 0.41 4.27E−13
TL rs109194156 5 12444024 0.21318 2.99 0.41 4.92E−13
TL rs110137797 5 12464607 0.21328 2.93 0.41 1.63E−12 Within TMTC2
TL rs109264225 5 12468154 0.21328 2.93 0.41 1.63E−12 Within TMTC2
TL rs43435142 5 12468826 0.21328 2.93 0.41 1.63E−12 Within TMTC2
UD rs42192551 29 49182244 0.46055 − 1.48 0.27 6.23E−08
UD rs110432804 6 89036570 0.46932 − 2.00 0.37 8.93E−08
UD rs108983037 6 88913092 0.46499 − 2.00 0.37 9.11E−08
UD rs110434046 6 88919352 0.46829 2.00 0.37 1.04E−07
UD rs137712965 6 88922396 0.46829 − 2.00 0.37 1.04E−07

Conformation trait EBV are standardized to have a mean value of zero and a standard deviation of 5

aTrait = body depth (BD), bone quality (BQ), chest width (CW), pin width (PW), rear attachment height (RAH), stature (ST), angularity (ANG), body depth (BD), dairy strength (DS), fore udder attachment (FA), front teat placement (FTP), pin setting (PS), rear attachment height (RAH), teat length (TL)

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