You are studying dog height

You are studying dog height. You compare 7 SNP loci between small & large dogs, but you collect data two different ways: 

1 Collect DNA from two different breeds: Miniature Dachshunds and Whippets. Dachshunds represent "small" dogs & Whippets "large" dogs. 

2 Collect DNA from multiple dog breeds, classifying each individual dog into either a "small" or "large" category. SNP loci 3, 5, and 6 are strongly associated with size in both the dachshund/whippet study and the multi-breed study. The SNP 1 locus is strongly associated with size in the dachshund/whippet study but is completely unassociated with size in the multi-breed study. Why would SNP 1 only show a strong association when using the dachshund/whippet group and not the multi-breed group?