resulting 20bp sequencing reads were mapped to the human genome sequence ( hg18 ) using an algorithm that we designed specifically to eliminate mappability biases between sequence variants . we divided the genome into 100 bp windows and selected the top 5% in terms of total dnasei sensitivity . dnasei sensitivity for each individual in each window was normalized by the total number of mapped reads for that individual . for qtl mapping , the data were further rescaled within and across individuals , and we adjusted the data for an observed individual  gc interaction , as well as for the top four principal components of the dnasei sensitivity matrix . genotypes for all available snps and indels were obtained from hapmap and 1000 genomes data and imputed where necessary . we performed dnase - seq association mapping by regressing the adjusted sensitivity in each window against the genotypes at variants in a 40 kb region centered on each dhs . as validation , we used our dnase - seq reads as well as chip - seq reads and dnase - seq reads from encode to confirm that allele - specific reads spanning heterozygous sites at dsqtls are consistent with the association analysis . we also used rna - seq data from the same cell lines to study the links between dsqtls and eqtls . finally , we explored the properties of dsqtls that make them more or less likely to influence gene expression by fitting a logistic model on all dsqtls , where the eqtl status of each dsqtl - eqtl test is modeled as a function of distance from the tss and a variety of other annotations . for full details of all methods
the mapping of expression quantitative trait loci ( eqtls ) has emerged as an important tool for linking genetic variation to changes in gene regulation1 - 5 . however 
 , it remains difficult to identify the causal variants underlying eqtls and little is known about the regulatory mechanisms by which they act . to address this gap , we used dnasei sequencing to measure chromatin accessibility in 70 yoruba lymphoblastoid cell lines ( lcls ) , for which genome - wide genotypes and estimates of gene expression levels are also available6 - 8 . 
 we obtained a total of 2.7 billion uniquely mapped dnase - seq reads , which allowed us to produce genome - wide maps of chromatin accessibility for each individual . 
 we identified 9,595 locations at which dnase - seq read depth correlates significantly with genotype at a nearby snp or indel ( fdr=10% ) . 
 we call such variants  dnasei sensitivity quantitative trait loci  ( dsqtls ) . 
 we found that dsqtls are strongly enriched within inferred transcription factor binding sites and are frequently associated with allele - specific changes in transcription factor binding . a substantial fraction ( 16% ) of dsqtls 
 are also associated with variation in the expression levels of nearby genes , ( namely , these loci are also classified as eqtls ) . 
 conversely , we estimate that as many as 55% of eqtl snps are also dsqtls . 
 our observations indicate that dsqtls are highly abundant in the human genome , and are likely to be important contributors to phenotypic variation .