Data for "Identification of genetic variants that affect histone modifications in human cells"

This webpage provides data for our paper on identifying and characterizing genetic variants associated with histone modification and Pol2 binding:

McVicker G*, van de Geijn B*, Degner JF, Cain CE, Banovich NE, Raj A, Lewellen N, Myrthil M, Gilad Y, Pritchard JK. "Identification of genetic variants that affect histone modifications in human cells". Science. 2013.

Raw Data

The ChIP-seq data generated by this study are available for download from GEO under accession GSE47991.

We also used RNA-seq, DNase-seq, and MNase-seq data from previous studies, which can be downloaded from GEO under accessions: GSE19480, GSE31388 and GSE36979.

Note that GEO does not make the fastq files available for download. To obtain fastq files you will need to download the SRA files, and convert them using the fastq-dump utility from NCBI's SRA-toolkit.

Processed Data

A subset of the input files we used to run the combined haplotype test are here (includes read counts, genotypes, etc.). If you need the complete set of input files, please let us know (they are quite large).

Results from applying the combined haplotype test genome-wide are here (includes histone modification and Pol2 QTLs at different FDR thresholds).

Input DNA

We did not use input DNA for our analyses, however, we did sequence a pooled sample of input DNA. This sample was not uploaded to GEO, but can be downloaded from here.

Source Code

Source code for the combined haplotype type test is available here.


For questions or to request code or additional data please contact Graham McVicker (, Bryce van de Geijn (, Yoav Gilad (, or Jonathan Pritchard (

Last updated 12/11/2013.