Eukaryotic DNA replication follows a strict spatiotemporal program, which intersects with gene regulation and shapes the mutational landscape. However, the genetic basis of the mammalian DNA replication timing program is poorly understood. In Chapter 2, I present an approach based on population genetics to study DNA replication timing in human cells. Specifically, I identify more than 1,500 replication timing quantitative trait loci (rtQTLs), i.e., genetic variants associated with inter-individual variation in DNA replication timing, in hundreds of human pluripotent stem cell lines. I reveal that a unique combination of histone modifications, composed of trimethylation on histone H3 lysines 4, 9 and 36, acetylation on H3 lysine 56, and histone hyperacetylation, shows enrichment at rtQTL locations. I further find that this unique “histone code” could predict locations of replication initiation in multiple human cell types, even for origins that are cell-type-specific. In addition, based on inter-individual variation in chromatin state, histone modification, and predicted transcription factor (TF) binding at rtQTLs in human embryonic stem cell lines, I identify positive (e.g., pluripotency-related TFs) and negative regulators (e.g., boundary elements) of DNA replication timing. I conclude that human DNA replication timing is controlled by a multi-layered mechanism that operates on target DNA sequences, is composed of dozens of effectors working combinatorially, and follows principles analogous to transcription regulation: a histone code, activators and repressors, and a promoter-enhancer logic. In Chapter 4, I present the first characterization of replication timing of the human Y chromosome and reveal a negative relationship between replication timing and mutation (both germline and within-cell-line, i.e., those mutations that arose somatically or during cell culture). Using within-cell-line mutation data from more than > 1,700 males, I uncover that mutation rate of the Y chromosome likely varies among human Y-chromosome haplogroups. Taken together, the findings presented in this thesis substantially improve our understanding into the causes and consequences of human DNA replication timing.