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. 2019 Oct 3;97(10):4066–4075. doi: 10.1093/jas/skz279

Table 1.

Final list of 105 SNPs selected for genotyping from a total of 175,490 SNPs

Genes SNP Chromosome SNP position Variant Consequence1 SIFT score2 SIFT prediction Protein Allele (one letter code) Protein allele (three letter code)
ADRM1 rs208332214 13 55418416 missense 0 deleterious T/N Thr/Asn
rs208566185 13 55427615 missense 0.84 tolerated Q/K Gln / Lys
rs208794152 13 55431510 missense 0.07 tolerated R/W Arg /Trp
rs209179785 13 55410932 missense 0.02 deleterious E/Q Glu/ Gln
rs211087002 13 55431496 missense 0.91 tolerated R/K Arg/ Lys
rs378318832 13 55407771 missense 1 tolerated S/P Ser/Pro
rs383024237 13 55407768 missense 1 tolerated C/R Cys /Arg
rs384785350 13 55407786 missense 0.82 tolerated S/A Ser/Ala
rs41696753 13 55424454 missense 0.04 deleterious R/Q Arg/ Gln
rs43770847 13 55415352 missense 0.29 tolerated S/G Ser/ Gly
rs446082190 13 55418674 missense 0.08 tolerated I/M Ile/Met
rs475020220 13 55421182 missense 0.01 deleterious K/T Lys/Thr
AGPAT6 rs110454169 27 36212557 5_prime_UTR
rs208675276 27 36212352 5_prime_UTR
rs379137591 27 36212515 5_prime_UTR
rs477793555 27 36212766 missense 0.06 tolerated K/N Lys/Asn
APOA1 rs134430767 15 27932525 missense 0.05 tolerated V/A Val/Ala
rs472309323 15 27932366 missense 0.48 tolerated V/A Val/Ala
APOA4 rs210304158 15 27907074 missense 1 tolerated H/R His /Arg
rs210921720 15 27907105 missense 0.08 tolerated Q/E Gln / Glu
APOA5 rs208297208 15 27866581 missense 0.55 tolerated E/D Glu/Asp
rs463483753 15 27868126 splice_donor
BCL2 rs462904013 24 62105166 missense 0.64 tolerated A/S Ala/Ser
C5orf34 rs208163974 20 31327150 missense 0.34 tolerated H/R His /Arg
rs209443540 20 31326810 missense 0.85 tolerated G/S Gly /Ser
CD44 rs210543167 15 66525817 missense 0.37 tolerated H/R His /Arg
rs42309927 15 66540981 missense 1 tolerated Q/P Gln /Pro
DDX11 rs109173661 5 107486607 missense 0.49 tolerated V/A Val/Ala
rs378943586 5 107487273 missense 0.29 tolerated M/I Met/ Ile
rs379141637 5 107497280 downstream_gene
rs482813209 5 107491924 missense 0.54 tolerated R/Q Arg/ Gln
DGAT1 rs109286048 14 1787761 missense 0.44 tolerated D/N Asp /Asn
rs109326954 14 1802266 missense 0.95 tolerated A/E Ala/ Glu
rs523413537 14 1802265 frameshift -/X (-/X
EPOR rs207986369 7 17003689 missense 1 tolerated A/P Ala /Pro
rs209618019 7 16984076 5_prime_UTR
rs466628285 7 16984149 5_prime_UTR
ESRRA rs477471785 29 43226583 downstream_gene
FKBP4 rs109367585 5 107451448 missense 0.78 tolerated M/T Met/Thr
rs110664228 5 107451447 missense 0.18 tolerated M/I Met/ Ile
rs134534391 5 107430855 missense 0.68 tolerated L/S Leu/Ser
rs449158440 5 107432580 missense 0.56 tolerated L/H Leu/His
rs476205399 5 107430347 missense 0.49 tolerated P/L Pro/ Leu
FOXM1 rs134093880 5 107375702 upstream_gene
rs135216344 5 107377538 upstream_gene
GHR rs109212162 20 31891025 missense 1 tolerated T/I Thr/ Ile
rs109300983 20 31891050 missense 0.09 tolerated S/G Ser/ Gly
rs110265189 20 31891130 missense 0.02 deleterious N/T Asn /Thr
rs385640152 20 31909478 missense 0.02 deleterious F/Y Phe /Tyr
HMGCS1 rs433464233 20 31472618 missense 0 deleterious Y/N Tyr/Asn
IL10 rs464052754 16 4406316 missense 0.62 tolerated T/S Thr/Ser
IL1B rs109004886 11 46417272 missense 0.07 tolerated G/D Gly /Asp
rs449928032 11 46411289 missense 0.62 tolerated I/V Ile/Val
rs477020822 11 46411299 stop_gained Y/* Tyr/*
IQSEC3 rs385440401 5 107639460 missense 0.39 tolerated P/L Pro/ Leu
rs432450632 5 107622167 missense 0 deleterious I/F Ile/Prohe
ITGB5 rs135061845 1 69889500 missense 0.23 tolerated K/R Lys/Arg
rs208109365 1 69899627 missense 1 tolerated A/E Al Ala / Glu
rs458450978 1 69832625 missense 0 deleterious D/G Asp /Gly
ITGB5 rs474996003 1 69852928 missense 0 deleterious H/P His /Pro
LDLRAP1 rs211106371 2 128082792 missense 0.44 tolerated P/L Pro/ Leu
MAN1C1 rs448142609 2 128007912 missense 0.47 tolerated A/G Ala / Gly
rs463343368 2 127909836 missense 0.02 deleterious S/R Ser/Arg
rs469242409 2 128007906 missense 0.57 tolerated V/G Val/ Gly
rs477509557 2 127915414 missense 0.42 tolerated V/M Val/Met
rs479080803 2 128007651 missense 0.35 tolerated H/P His /Pro
rs482632351 2 128007909 missense 0.3 tolerated Q/P Gln /Pro
rs482762432 2 127888951 missense 0.02 deleterious L/P Leu/Pro
MAP3K5 rs109478031 9 75560882 missense 0.45 tolerated D/N Asp /Asn
MRPS30 rs135415772 20 30081437 missense 1 tolerated T/A Thr/Ala
NNT rs449852282 20 31204527 missense 0.08 tolerated A/P Ala /Pro
rs478597655 20 31257968 5_prime_UTR
OSBPL2 rs383712095 13 55450613 missense 0.23 tolerated N/K Asn / Lys
rs41696759 13 55450615 missense 1 tolerated N/D Asn /Asp
PAPPA rs43580134 8 107186321 missense 1 tolerated M/T Met/Thr
rs43580135 8 107186299 missense 0.52 tolerated T/A Thr/Ala
rs43580136 8 107186285 missense 0.15 tolerated A/V Ala /Val
PARP11 rs476004287 5 106624500 missense 0.05 deleterious P/R Pro/Arg
PPARG rs109613657 22 57367375 missense 1 tolerated Q/H Gln /His
rs132979274 22 57402368 stop_gained Q/* Gln /*
rs42016945 22 57468357 5_prime_UTR
RHNO1 rs210028143 5 107353582 missense 0.73 tolerated A/T Ala /Thr
SLC17A9 rs440569152 13 54923249 missense 0.05 tolerated Y/S Tyr/Ser
rs472517979 13 54917820 missense 0.02 deleterious S/R Ser/Arg
TEAD4 rs133238643 5 107296229 5_prime_UTR
rs384581336 5 107325259 5_prime_UTR
TEX14 rs109393617 19 9775707 missense 0.22 tolerated T/A Thr/Ala
rs110989707 19 9775272 missense 0.23 tolerated T/A Thr/Ala
rs134356175 19 9742447 missense 0.64 tolerated P/L Pro/ Leu
rs134816249 19 9777840 missense 0.21 tolerated N/S Asn /Ser
rs208759383 19 9788622 missense 1 tolerated M/L Met/ Leu
rs378060964 19 9767815 missense 0.13 tolerated G/R Gly /Arg
rs380796779 19 9789924 missense 0 deleterious G/R Gly /Arg
rs383432764 19 9792619 missense 0.19 tolerated R/W Gly /Trp
rs460269897 19 9775646 missense 0.2 tolerated H/P His /Pro
TLR4 rs29017188 8 108829143 5_prime_UTR
rs516362864 8 108829405 frameshift -/X -/X
rs8193069 8 108838685 missense 0.28 tolerated T/I Thr/ Ile
TRPS1 rs381800291 14 50862411 missense 0.09 tolerated D/N Asp /Asn
rs468711225 14 50863245 splice_donor
TSPAN11 rs110381847 5 106978486 5_prime_UTR
rs110799905 5 106978562 5_prime_UTR
rs134575400 5 106976010 5_prime_UTR
rs135745883 5 107005431 missense 1 tolerated I/V Ile/Val
rs210073944 5 107030616 missense 0.12 tolerated D/N Asp /Asn

1SNP consequence obtained using Ensembl Biomart database (Ensembl 83, Bos taurus UMD3.1, http://useast.ensembl.org/Bos_taurus/Info/Index).

2SIFT score: Sorts intolerant from tolerant algorithm score and the SIFT score ranges from 0.0 (deleterious) to 1.0 (tolerated).