Table 1. HMX1 sequence variants.

HMX1	Variant on BTA 6 (UMD3 assembly)	cDNA	protein	genotype	Highland cattle cases controls		other breed controls
highly	g.106719992G>delG			G/G		78	88
conserved				G/delG	36	1	46
region				delG/delG	3		10
	g.106720058_106720133dup			wt/wt		80	144
				wt/dup	39
				dup/dup	1
Exon 2	g.106868441T>G	c.835A>C	p.M279L	T/T
				T/G
				G/G	2	4
	g.106868626G>T	c.650C>A	p.P217Q	G/G
				G/T
				T/T	2	4
	g.106868630T>A	c.646A>T	p.I216F	T/T
				T/A
				A/A	2	4
Exon 1	g.106871834G>A	c.299C>T	p.P100L	G/G		2	32
				G/A	23		16
				A/A	5		1
	g.106871880G>C	c.253C>G	p.A85P	G/G			1
				G/C			15
				C/C	25	48	33
	g.106871897G>C	c.236C>G	p.G79A	G/G			7
				G/C		6	18
				C/C	25	42	24

Coding variants in the HMX1 gene and structural non-coding variants in the HMX1 associated highly conserved region. Note that the 76 bp duplication is perfectly associated with crop ears (bold face).