Many adult-onset diseases are caused by genetic variants that have proximal effects at the earliest stage of development – the pluripotent, ground state. In order to better understand the role of genetics in maintenance of pluripotency, we performed genetic and genomic analysis on a panel of undifferentiated embryonic stem cell lines derived from genetically heterogeneous Diversity Outbred mice (DO mESCs). We profiled chromatin accessibility (ATAC-seq) and transcript abundance (RNA-seq) of each DO mESC line maintained in cell culture conditions that promote the pluripotent state. We mapped thousands of loci with genetic variants that alter chromatin accessibility (caQTL) and transcript abundance (eQTL). Many distant QTL co-localize and appear as prominent trans-bands, suggesting that a common regulator may drive them. One locus on chromosome 15 altered the expression of 208 genes including many with known functions in maintenance of pluripotency. We applied mediation analysis and identified Lifr (leukemia inhibitory factor receptor) transcript abundance as the causal intermediate for these eQTL. Interestingly, sex-specific differences in many of these genes suggest a nonlinear response to Lifr dosage. Joint mediation analysis of eQTL by chromatin accessibility revealed a variable region of open chromatin upstream of the Lifr gene containing a single SNP that predicts the allelic effects on Lifr expression and its downstream targets. This suggests a causal chain of molecular events starting from a single SNP that modulates chromatin state in a Lifr enhancer that in turn affects Lifr transcription, which ultimately regulates transcript abundance of 208 target genes, including both known and novel pluripotency-associated genes. To validate these predictions and demonstrate their effects on ground state pluripotency and early lineage commitment, we have developed complimentary genetic resources including F1 hybrid mESC lines from Collaborative Cross strains and CRISPR-modified inbred, founder mESC lines. Future studies will integrate additional cellular assays within this renewable systems genetic resource to expand our understanding of genetic influence on differentiated cell types and ultimately to fetal and adult in vivo phenotypes.