available. The chromatin state represents the accessibility of genomic regions (every 200bp) with 15 categorical states predicted by a hidden Markov model based on 5 chromatin marks for 127 epigenomes in the Roadmap Epigenomics Project46. A lower state indicates higher accessibility, with states 1–7 referring to open chromatin states. We annotated the minimum chromatin state across tissues to SNPs. The 15-core chromatin states as suggested by Roadmap are as follows: 1=Active Transcription Start Site (TSS); 2=Flanking Active TSS; 3=Transcription at gene 5’ and 3’; 4=Strong transcription; 5= Weak Transcription; 6=Genic enhancers; 7=Enhancers; 8=Zinc finger genes & repeats; 9=Heterochromatic; 10=Bivalent/Poised TSS; 11=Flanking Bivalent/Poised TSS/Enhancer; 12=Bivalent Enhancer; 13=Repressed PolyComb; 14=Weak Repressed PolyComb; 15=Quiescent/Low. Standardized SNP effect sizes were calculated for the most impactful SNPs by transforming the sample size-weighted meta-analysis Z score, as described by Zhu et al.47.
