Pooled CRISPR screens identify genes and non-coding genomic regions that regulate red blood cell density

Genome-wide association studies have identified >1000 loci associated with red blood cell (RBC) traits. However, few of these associations have been functionally characterized. Here, we performed pooled CRISPR screens in an erythroid cell line to identify genes and regulatory non-coding sequences that control RBC density. We perturbed 556 candidate genes and genomic sequences near 2114 GWAS variants. After validation, we found 17 genes and 13 regions near GWAS variants, implicating known (e.g. ATP2B4 , CCND3 , EPOR ) and novel (e.g. CHTF8 , CTU2 , DNASE2 , RAB10 ) genes. We confirmed that deletions in the osmotic stress response kinase gene OXSR1 increase cell density. We also combined CRISPR perturbations and RNA-sequencing to show how a non-coding genomic sequence near rs13255015 regulates the expression of the transcription factor ZFAT in cis and SLC4A1 in trans . Our results suggest experimental strategies to characterize GWAS findings and provide new molecular insights into the regulation of complex RBC traits.