Type of analyses Which can be performed on Whole Genome Data

Hey everyone,
This might be a nieve question, kindly spare me. I want to know about type of analyses which can be performed on whole genome sequence data.
For example, say I have whole genome data of like 4 different cattle breeds of xyz country. The one analysis i know that can be performed is Variant (SNP,Indel) analysis. I want to know what else i can do with that sequence data.
Any analysis name or pipeline which can be used for further insights into the data ?
Help will be greatful.
Thank you.