Robert Thurman et. al,

"The accessible chromatin landscape of the human genome"

Nature, 489, pp. 75-82, 5 Sep. 2012

Downloadable Data

Much of the data presented in the paper is available via the public FTP server using anonymous login, at See the supplement for details. This site contains items not available on the public server.

Further annotation of master list

The paper references extensively a so-called "master list" of 2,890,742 unique, non-overlapping DHS positions that span the DHS landscape of all 125 cell-types probed. As described in the supplement, the full master list (in addition to the DHS called on each individual cell-type) is available on the EBI public ftp site, at
See file
The master list is annotated in column 4 with the number of cell-types having a DHS overlap at that position. In addition, we have the names of the cell-types that overlap at each position, in the following file. There is one row per master list peak, in the same order as the master list, with cell-type names separated by a semi-colon.

Addendum to Supplementary Table 7

This table of correlated distal/promoter DHS pairs was created using TSSs of transcripts from Gencode v. 7. Only TSSs with confidence levels of 1 and 2 were used (1 = validated, 2 = manually annotated). Specifically, TSSs with confidence level 3 (automated annotation) were not used. The PAH gene, shown in Figure 5a of our paper, was labeled "level 3" in Gencode v.7, and thus does not appear in Supplementary Table 7. The distal DHSs correlated with the PAH promoter DHS can be found here.

Promoter Predictions

The public FTP site appears to have some inaccessible subdirectories with regards to the DNaseI/H3K4me3 promoter predictions. Therefore, we include the full set of predictions here.