Table 2

Summary of information available for the Highest 1% SNPs selected by the stepwise regression
dbSNP1 Chr2 Position % dEBV3 Genes4in ± 250Kb Fat-related QTL5 QTL reference
rs133046994 10 18129602 11.12 THSD4, LRRC49 SF, MS [65,66]
rs137294146 1 132385787 9.41 SOX14, CLDN18, DZP1L FT12R, IF [29,71]
rs109349988 3 15814096 5.21 KCNN3, EFNA3, EFNA4, DCST2, LOC100294774, PMVK, ADAR, CHRNB2, ADAM15, ZBTB7B, LOC100294857, DCST1, FLAD1, PYGO2, CKS1B, PBXIP1, SHC1, LOC100294894 FT12R, MS [66]
rs136717249 19 37969870 4.88 B4GALNT2, GNGT2, ABI3, PHOSPHO1, ZNF652, NGFR, PHB, IGF2BP1, GIP OAC, PAC [84,85]
rs134790147 13 20780821 3.51 CCDC7, ARL5B, MGC152301, LOC100848675, LOC100847992 FT12R [29]
rs136287610 25 42678992 2.89 FAM20C, LOC783396, LOC100300875, LOC100337322, PRKAR1B, PDGFA, PTCHD3, LOC783852, LOC783961 FT12R [29]
rs136393667 11 65619399 2.51 LOC786621, LOC100139826, ETAA1 FT12R, MS [29]
rs41790889 16 990255 2.07 OPTC, PRELP, FMOD, BTG2, LOC789413, LOC789394, CHI3L1, MYBPH, ADORA1, LOC100847554 FT12R, MS [29]
rs42126516 4 52535108 1.99 TFEC, LOC100296613, TES MS [29,97]
rs42021729 3 64737352 1.46 MS [98]
rs137001098 8 95507919 1.46 SMC2, LOC100337180 MS [29]
rs43341824 1 50110036 1.23 LOC785980, ALCAM OAC, FT12R [85,99]
rs41683753 13 33219105 1.04 CACNB2, NSUN6, EPC1, LOC10084770 PAC, MS [29,85]
rs136348926 12 10043410 0.90 LOC786945
rs109869647 3 13195543 0.72 LOC100849046, LOC100848852, LOC784007, LOC783963 MS [66]
rs110833507 11 42856561 0.69 LOC100296234, LOC100296682, BCL11A
rs42923911 2 12761205 0.57 LOC787311, LOC100848878
rs135638125 10 18147174 0.55 THSD4, LRRC49 MS, SF [65,66]
rs110607520 9 96622647 0.66 SYTL3, TULP4, TMEM181, EZR, LOC781263, DYNLT1, RSPH3, LOC782714, TAGAP, LOC782637 MS [29]
rs110025080 9 11710300 0.52 RIMS1
rs109697559 2 61906393 0.58 LOC100847709, LOC100297008, LCT, UBXN4, MCM6, DARS, R3HDM1, MIR128-1 MS [29]

1 Reference SNP cluster report.

2 Chromosome in B. taurus.

3 % dEBV variance is the model R2 for each of the SNPs in the final analysis which fits all SNPs as fixed effects into a regression analysis.

4 Gene symbol.

5SF subcutaneous fat, FT12R fat thickness at the 12th rib, IF intramuscular fat, FT fat thickness, MS marbling score, OAC oleic acid content, PAC palmitoleic acid content.

Mokry et al.

Mokry et al. BMC Genetics 2013 14:47   doi:10.1186/1471-2156-14-47

Open Data