The ENCODE Project Consortium has systematically mapped regions of transcription, transcription factor association, chromatin structure, and histone modification in the human genome, enabling the assignment of biochemical functions to 80% of the genome, including non-coding regions. These data reveal that 95% of the genome lies within 8 kb of a DNA-protein interaction, and 99% is within 1.7 kb of a biochemical event. The project identified 399,124 enhancer-like regions and 70,292 promoter-like regions, along with many quiescent regions. RNA production and processing correlate with chromatin marks and transcription factor binding, indicating that promoter functionality explains most RNA expression variation. Many non-coding variants lie in ENCODE-annotated regions, and disease-associated SNPs are enriched in non-coding functional elements. The project also identified 1.64 million data sets to annotate functional elements across the entire human genome, revealing complex gene regulation mechanisms and chromatin interactions. The ENCODE project has developed methods to map functional elements across the human genome, including RNA transcribed regions, protein-coding regions, transcription factor-binding sites, chromatin structure, and DNA methylation. These data show that 80.4% of the human genome is covered by at least one ENCODE-identified element, with regions of histone modification covering 56.1% of the genome. The project also identified 127,417 promoter-centered chromatin interactions in K562 cells, showing complex gene-element connectivity. The integration of ENCODE data with known genomic features reveals that transcription factors are nonrandomly distributed across the genome, with co-associations between transcription factors and other genomic features. The project has identified 3,307 pairs of statistically co-associated factors, with some associations more specific to promoter or intergenic regions. The integration of ENCODE data with other genomic features has provided new insights into the organization and regulation of the human genome, and is an expansive resource for biomedical research.The ENCODE Project Consortium has systematically mapped regions of transcription, transcription factor association, chromatin structure, and histone modification in the human genome, enabling the assignment of biochemical functions to 80% of the genome, including non-coding regions. These data reveal that 95% of the genome lies within 8 kb of a DNA-protein interaction, and 99% is within 1.7 kb of a biochemical event. The project identified 399,124 enhancer-like regions and 70,292 promoter-like regions, along with many quiescent regions. RNA production and processing correlate with chromatin marks and transcription factor binding, indicating that promoter functionality explains most RNA expression variation. Many non-coding variants lie in ENCODE-annotated regions, and disease-associated SNPs are enriched in non-coding functional elements. The project also identified 1.64 million data sets to annotate functional elements across the entire human genome, revealing complex gene regulation mechanisms and chromatin interactions. The ENCODE project has developed methods to map functional elements across the human genome, including RNA transcribed regions, protein-coding regions, transcription factor-binding sites, chromatin structure, and DNA methylation. These data show that 80.4% of the human genome is covered by at least one ENCODE-identified element, with regions of histone modification covering 56.1% of the genome. The project also identified 127,417 promoter-centered chromatin interactions in K562 cells, showing complex gene-element connectivity. The integration of ENCODE data with known genomic features reveals that transcription factors are nonrandomly distributed across the genome, with co-associations between transcription factors and other genomic features. The project has identified 3,307 pairs of statistically co-associated factors, with some associations more specific to promoter or intergenic regions. The integration of ENCODE data with other genomic features has provided new insights into the organization and regulation of the human genome, and is an expansive resource for biomedical research.