Step 1: Recall the genetics of the renal cell carcinoma subtypes. Each major subtype has its own chromosomal signature, which is the basis of this question.
Step 2: Assign the signatures. Clear cell carcinoma, the commonest type, is linked to the VHL gene on chromosome 3p, so it shows 3p deletions and VHL mutations. Papillary carcinoma shows trisomy of chromosomes 7 and 17 and loss of Y.
Step 3: Identify chromophobe. The chromophobe variant is characterized by multiple chromosome losses, classically monosomy of chromosomes 1 and Y and other monosomies, producing a hypodiploid genome.
Step 4: Eliminate the wrong options. VHL mutation and 3p deletion belong to clear cell carcinoma. Trisomy 7 and 17 belongs to papillary carcinoma. Only monosomy of 1 and Y fits chromophobe.
Conclusion: The chromophobe variant is associated with monosomy of 1 and Y. The answer is option D.