Sequenced-based GWAS for linear classification traits in Belgian Blue beef cattle reveals new coding variants in genes regulating body size in mammals

Table 2 Annotation of candidate or lead variants for the 11 QTL regions

BTA	Position	REF	ALT	Frequency	Gene	Consequences	SIFT score	GERP score	Phastcons
3	95,015,373	T	C	0.050	RNF11	Splice site variant		0.862	0.976
4	112,030,024	T	C	0.470	EZH2	Missense variant I549M	0.03	0.222	1
5	105,769,735	C	T	0.700	CCND2	Regulatory (ATAC-Seq, eQTL)		− 4.2	0
6	36,226,849	A	AT	0.050		Intergenic variant		0.078	–
14	76,227,910	C	T	0.140	WWP1	Missense variant R844Q	0.00	0.530	1
16	57,725,284	C	A	0.720	PAPPA2	Missense variant P282T	0.00	–	1
18	1,673,649	A	AT	0.270		Regulatory (ATAC-Seq)		0.149	–
19	47,095,175	CAG	C	0.030	MRC2	Frameshift variant		0.504	0
23	9,716,619	G	A	0.480	ARMC12	Regulatory (ATAC-Seq, eQTL)		− 0.678	–
25	25,933,247	G	A	0.010	ATP2A1	Missense variant R559C	0.00	0.222	0.984
26	45,553,105	G	A	0.590	ADAM12	Missense variant A582V	0.03	1.220	0.890

The frequency is reported for the alternate allele and SIFT scores are provided for missense variants
BTA Bos taurus chromosome, REF reference allele, ALT alternate reference

ISSN: 1297-9686