Polymorphisms that affect chr21 gene expression have significance for both variable severity in Down syndrome and common multifactorial conditions. Results here demonstrate "selective homolog silencing" in cells from even one individual can provide a valuable complement to large studies. In trisomic iPSC subclones that silence different chr21 homologs (via -based silencing), we discovered unusually large, homolog-specific, differences in in iPSCs, cortical organoids and endothelial cells. RNA FISH showed transcription almost entirely from the H1 homolog, correlated with CpG promoter methylation differences. Polymorphisms different on H1 versus H2/H3 had strongest eQTLs in GTEx, especially in brain. Collective results indicate RWDD2B functional dosage is more frequently disconnected from copy number even compared to neighboring genes. RWDD2B function is unknown, but nearby methyl-eQTLs are implicated in osteoarthritis, and potential roles in inflammation or immune response merit consideration. This study has significance for RWDD2B regulation and demonstrates a cell-based methodology to study polymorphisms.