Matt Maurano, Richard Humbert et. al,

"Systematic Localization of Common Disease-Associated Variation in Regulatory DNA"

Science, 337, no. 6099, pp. 1190-1195, 7 Sep. 2012

Downloadable Data

DNaseI hypersensitive sites (DHSs), FDR 5% hotspots

Below find the DHS bed files (hg19 coordinates) for each of the 349 samples listed in Table S1 of the paper. Note the bedfiles in the GEO accessions referenced in the paper have a slightly different filtering. The files thresholded at FDR 5% linked here are the exact tracks used for the paper.

DHS-to-promoter assignments based on cross-cell-type hypersensitivity correlations

This analysis was presented in Tables 1, S4-S7, Fig 2A, and Section 4.1 of SOM.

The SOM PDF included only correlated DHSs overlapping GWAS SNPs (Table S7). Here is the complete set of 1,073,959 DHSs correlated in the 35 clustered cell types new to Maurano et al.
This file includes genomic coordinates (hg19) of all promoter DHSs and distal, non-promoter DHSs within ±500 kb correlated with them at threshold 0.7. The file format is the same as described for Supplementary Table 7 of the Thurman et al. Nature 2012.
The vectors of peak heights from which the correlations were calculated are available in this file. This file contains consensus DHS coordinates across the genome;
it is a superset of the data used for the correlation analysis. The vectors are given as comma-delimited lists in column 4. The list order is given in Table S5.

Table S6 drew from assignments originally presented in Thurman et al. Nature 2012. For convenience, here is a link to the complete set of correlated DHSs for this set of cell types. This set is described in Supplementary Table 7 of the SOM.
The vectors of peak heights from which the correlations were calculated are available in this file. This file contains consensus DHS coordinates across the genome;
it is a superset of the data used for the correlation analysis. The vectors are given as comma-delimited lists in column 4. The list order is given in Table S4.

Protocols


The protocols we followed when processing the following cell lines (see Table S1) can be found in the accompanying links.

Supplemental tables in tab-delimited format

Some of the tables included in the supplemental material PDF were quite long. For your convenience, here they are tab-delimited format. * Tables S6 and S7 also include a new column not in that PDF describing the location (hg19) of the DNaseI hypersensitive site correlated with the SNP DNaseI hypersensitive site. Note that table S7 is sorted slightly differently than the SOM, otherwise the contents are the same.