This is a companion package for SNPhood and provides additional example datasets for the SNPhood package. The datasets in the SNPhoodData package are used in the SNPhood vignette and provide “real-world” examples for exploring the molecular neighbourhood of SNPs using allele- and genotype-specific analyses.
In a recent study we have identified thousands of quantitative trait loci (QTLs) for different histone marks using individuals from the Yoruban (YRI) population . In our case, histone (h)QTLs are SNPs for which the genotype correlate with the variation of histone H3K27ac signal within a H3K27ac peak. Here we will investigate how many of these previously identified hQTLs show allele-specific binding in individuals from a different population (CEU; European).
The example dataset consists of the following files:
For an example workflow, see the workflow vignette of the SNPhood package.
 Grubert, F., Zaugg, J. B., Kasowski, M., Ursu, O., Spacek, D. V., Martin, A. R., … & Snyder, M. (2015). Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions. Cell, 162(5), 1051-1065.
 Kasowski, M., Kyriazopoulou-Panagiotopoulou, S., Grubert, F., Zaugg, J. B., Kundaje, A., Liu, Y., … & Snyder, M. (2013). Extensive variation in chromatin states across humans. Science, 342(6159), 750-752.
 1000 Genomes Project Consortium. (2010). A map of human genome variation from population-scale sequencing. Nature, 467(7319), 1061-1073.