No. of genes in chromosomes. phenotype
This may have to do with the fact that the cells require 'housekeeping genes', which are typically constitutive genes that are expressed in all cells of an organism under normal and patho-physiological conditions. Housekeeping and other essential genes are distributed uniformly across different chromosomes thereby making any chromosome indispensable. 

"Housekeeping genes are genes that are required for the maintenance of basal cellular functions that are essential for the existence of a cell, regardless of its specific role in the tissue or organism. Thus, they are expected to be expressed in all cells of an organism under normal conditions, irrespective of tissue type, developmental stage, cell cycle state, or external signal." 
http://www.cell.com/trends/genetics/pdf/S0168-9525(13)00089-9.pdf 

Intriguingly, chromosome X lacks housekeeping genes. A recent study suggested a possible explanation for this, as follows: "In the end, we have found the answer to be quite simple. Whereas most chromosomes operate in pairs, meaning there are two copies of each gene in every cell, in contrast, we only have one active copy of the X chromosome. This means it is not sustainable for highly active genes to be on the X chromosome. Housekeeping genes tend also to be highly active – they just couldn't survive on the X.”
http://www.bath.ac.uk/news/2016/01/12/x-chromosome/

Gene expression is regulated through transcriptional and translational regulation of genes to generate tissue-specific mRNA. Moreover, through alternative splicing a gene can code for multiple types of proteins. Alternative pre-mRNA splicing is widely used by (higher) eukaryotes to generate different protein isoforms in specific cell or tissue types. This means that the same gene can have different gene products in different cell types.

"Alternative splicing is a mechanism for generating a versatile repertoire of functionally different proteins within individual cells. The significance of alternative splicing is clearly evident in highly specialized cells such as neurons. For example, all of the main neurotransmitter receptors contain subunits that are alternatively spliced, which influences their localization, as well as their ligand-binding, signal-transducing and electro-physiological properties." 
http://www.nature.com/nrn/journal/v2/n1/full/nrn0101_043a.html
http://nar.oxfordjournals.org/content/30/17/3754.short 
http://genomebiology.biomedcentral.com/articles/10.1186/gb-2004-5-10-r74

Protein-coding sequences account for only a very small fraction of the genome (approximately 1.5%), and the rest is associated with non-coding RNA molecules, regulatory DNA sequences, LINEs, SINEs, introns, and sequences for which as yet no function has been determined. Furthermore, gene expression is controlled by regulatory elements that can be located far away along the same chromosome or in some cases even on other chromosomes. Genes and these regulatory elements physically associate with each other resulting in complex genome-wide networks of chromosomal interactions. 
https://en.wikipedia.org/wiki/Human_genome 
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2653627/

The genome is very intricate and consists of elements that interact with each other to regulate gene expression and to carry out various functions. Loss of any of these elements may affect other elements and disrupt cellular homoeostasis, resulting in cellular dysfunction, death or cancer.

I hope this somewhat answers your question.