Genomics data alone provides only partial insights into the cell’s type, state, or function. To obtain a more complete picture and reveal the cell’s phenotypic character, a multi-omics approach is needed that expands beyond DNA profiling. Here, we demonstrate for the first time, that the Tapestri Platform enables the detection of genomic variants and protein expression simultaneously from the same cell. Genomic variations, such as single nucleotide variants (SNVs) and copy number variations (CNVs), are now co-detected with proteins. This novel capability has the power to reveal rare cell populations, subtle cell states, and link genomic variation to protein expression, leading to more informed research on disease and therapeutic development.