Supplementary Information containing supplementary methods, figures and tables with their legends from Integrative Genomic Analysis Predicts Causative <i>Cis</i>-Regulatory Mechanisms of the Breast Cancer–Associated Genetic Variant rs4415084

Abstract

<p>Supplementary Information containing supplementary methods, figures and tables with their legends. This file includes: Supplementary Materials and Methods; Supplementary Table 1 - Breast cancer cell line DNase-seq data used for SNP prioritization; Supplementary Table 2 - Breast cancer cell line ChIP-seq data used in this study; Supplementary Table 3 - Transcription factor motif databases used in this study; Supplementary Table 4 - A comparison of eQTL genes for all three 5p12 breast cancer GWAS SNPs; Supplementary Table 5 - eQTL results of rs4415084 for genes within TAD; Supplementary Table 6 - Significant isoform-QTL results of rs4415084; Supplementary Table 7 - Differential chromatin interaction analysis between MCF-7 and T-47D based on Hi-C data; Supplementary Figure 1 - A schematic representation of the phasing certainty measure in local chromosome allele-specific expression (LCASE) analysis; Supplementary Figure 2 - A schematic representation of TF prioritization based on TF-gene expression correlation analyses; Supplementary Figure 3 - Transcription elongation downstream of MRPS30; Supplementary Figure 4 - eQTL results for rs4415084 based on normal breast tissue data from GTEx; Supplementary Figure 5 - LCASE SNPs in MRPS30 processed transcripts; Supplementary Figure 6 - LCASE SNPs in RP11-53O19.3; Supplementary Figure 7 - LCASE SNPs in RP11-53O19.1; Supplementary Figure 8 - Other candidate causative SNPs and TFs.</p>