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. 2013 Mar 20;8(3):e59251. doi: 10.1371/journal.pone.0059251

Table 1. Target SNP interactions and filter information.

Filtering results
Diagnostic SNP interaction Weaver Allele
Position SNP Weaver allelea TFBSb Bovine ESTc Non-bovine mRNA dbSNPd Not homozyougs in affected Homozygous in non-affected Frequency >0.06 in non-affected Frequency >0.00 in control breeds Homozygous in all animals Homozygous in progeny confirmed carriers SNP call rate <0.90 No genotype produced
48007166 A/G G X
48007166 A/G – X
48232691 G/A – X X X
48337968 G/A – X
48402338 C/A C X X
48486736 C/T – X X X
48512459 T/C C X X
48615216 T/C – X X X
48622306 C/A – X X X
48732707 T/A – X X X
48735699 T/C – X X X
48901850 C/T – X X X
48947509 T/C T X
48955770 C/T T X X
49037435 G/A A X X
49114986 C/T C X X X
49138874 A/G A X
49244789 G/A G X X X
49247979 T/G T X X X X
49258127 T/C T X X X
49290010 T/G T X
49310747 A/C C X X X X
49323692 T/C T X X
49331946 C/T C X X
49388225 A/C A X X X X
49389293 T/C T X X X X
49403179 C/G C X X X X
49526344 C/T C X
49651768 G/A G
49653001 T/C T X
49656945 T/C T Xe rs109982331
49657798 G/A A X
49664852 T/C T X
49667361 T/C T rs109664911
49673503 T/C T rs109895716 Xg
49681169 T/C C Xg
49682552 G/A G X rs110232598 Xg
49686038 G/A G Xg
49687224 G/T G Xg
49687585 T/C T rs110652080 Xg
49691015 G/T T X rs109108372 Xg
49691127 T/C C X X
49692015 C/T C Xg
49692485 T/G T rs108969425 Xg
49692825 T/C T rs110864204 Xg
49693121 T/C C Xg
49693140 G/T T Xg
49693164 T/A T Xg
49693178 C/A C Xg
49693265 G/A G Xg
49693284 G/A A Xg
49693601 T/C C Xg
49693913 C/A C Xg
49694977 G/A G Xg
49695504 G/A A rs110503389 Xg
49695952 T/C T rs110633416 Xg
49698002 T/C T rs109252615 Xg
49698436 T/C T Xg
49700154 G/A A Xg
49701106 T/C C Xg
49702287 T/C C rs109980500 Xg
49702494 G/A A Xg
49704844 G/A G X Xg
49705951 G/A G X Xg
49706022 T/C C Xf Xg
49708283 T/C C Xg
49715678 T/C T X rs109748527 Xg
49718641 T/C T rs109194289 Xg
49850942 G/A A X
49878773 T/C T
49906971 G/T G X X
49959480 A/G A X X
49976213 G/T G X X
50223808 T/C C X X X
50274978 G/A G X X
50298949 C/T C X X
50312908 G/A G X X
50333552 T/C T X X
50360030 A/C A X X
50366763 A/G – X X X
50367956 T/A T X X
50369238 G/A A X X
50379409 A/G G X
50379409 A/G – X
50380664 G/T T X X
50393360 T/C T X X X
50398187 G/A A X X X
50398280 T/C T X X X
50402642 G/C G X X X
50455808 T/C T X X X
50472537 G/A A X
50475447 G/A G X
50481151 G/A G
50534843 G/T G X X
50541402 T/C T X
50543512 T/C T X X
50552996 G/A G X X
50553258 G/A G X X
50554161 T/C C X X
50557292 G/A A X X
50557504 T/C T X X
50561765 G/A A X X
50564926 T/A T X X
50567814 T/C T X X X
50608260 A/G – X X
50634196 T/C C rs111022650 X
50634196 C/T – X
50644398 G/A A X
50675770 T/C C X
50705601 A/C A X X
50705673 C/A C X X X
50728982 T/A T X X X
50741937 G/A G X X X X
50752507 C/T C X X
50755178 A/G A X X
50757722 A/G A X
50758316 G/A G X X
50759242 T/C T X X
50769426 G/T G X X
50771856 T/C C X X
50772507 A/G A X X
50772537 A/G A X X
50774184 T/G T X
50774778 T/C T X X
50774884 C/T C X X
50775126 C/T C X X
50779324 G/A G X X X
50790384 A/G A X X X X
50796591 A/G A X X
50858538 A/G A
50929556 G/A G
51077321 T/C T X
51096233 G/A G X X X
51216265 T/C T X X
51387621 G/C C X
51395221 G/A G X
51828149 T/C C X X X
51836464 G/C C X
52023948 A/G A X
52447753 A/C C X X
52488585 G/C G X
52561658 T/C C X
52588273 C/T C X
52594374 G/A G X X X X
52614817 T/C T X X X X
52615034 C/A C X X X X
52849464 G/A G X X X
52851362 A/G A X X X
52853963 T/C T X X X
52895919 A/G A X X X X
52900386 T/C T X X X
52934522 T/C T X X X
52934540 C/T C X X
52938145 T/G T X X X
52967096 A/G A X
52976777 T/G T X X
a

The homozyous allele in affected animals.

b

Affected predicted TFBS information in Table 3.

c

Bovine EST: AJ677346.

d

None of the listed dbSNP IDs are validated.

e

mRNA (n = 56) at SNP 49656945, partial list: JO339806, JU559277, JV452054, AK382080, BC024441, AK231430.

f

mRNA (N = 4) at SNP 49706022: JO339806, JO397144, AK382080, JO62179.

g

SNP is heterozygous in one Holstein bull with 4% non Holstein genomic influence.