Construction and characterization of the STARR-seq library. (A) Schematic of the STARR-seq library design. A candidate set of 198-bp oligos was selected based on their overlap with binding (b)QTLs, histone mark (hm)QTLs, chromatin accessibility (ca)QTLs, and cis-eQTLs. Reference and alternative variants were cloned into a plasmid vector under origin of replication core-promoter. The reporter library was transfected into cultured teloHAECs, and deep sequencing was conducted. The enrichment of reporter RNA expression over the input DNA library directly and quantitatively reflects enhancer activity. (B) Chromatin state distribution of the STARR-seq library regions across the core set of ENCODE samples. STARR-seq library regions were intersected with previously published genome-wide chromatin partitioning into 18 chromatin states by ChromHMM. (C) STARR-seq library regions that overlap an enhancer, relative to the total number of enhancers called in the sample. Enhancer coordinates and sample grouping were obtained from EpiMap. (D) Sharing of STARR-seq library enhancers and promoters across a diverse set of epigenomes. STARR-seq library regions were intersected with the ChromHMM chromatin states (18-state model) for every sample in EpiMap, an epigenetic compendium spanning the human body. For each STARR-seq region, the number of samples with a promoter or enhancer overlap was counted. The different enhancer states (active, bivalent, genic, and weak) were combined, as were the promoter states (active TSS, bivalent TSS, flanking TSS, flanking TSS upstream, and flanking TSS downstream).
