title: SNPhood: investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data.
abstract: The vast majority of the many thousands of disease-associated single nucleotide polymorphisms (SNPs) lie in the non-coding part of the genome. They are likely to affect regulatory elements, such as enhancers and promoters, rather than the function of a protein. To understand the molecular mechanisms underlying genetic diseases, it is therefore increasingly important to study the effect of a SNP on nearby molecular traits such as chromatin or transcription factor binding.
  
  
  
  We developed SNPhood, a user-friendly Bioconductor R package to investigate, quantify and visualise the local epigenetic neighbourhood of a set of SNPs in terms of chromatin marks or TF binding sites using data from NGS experiments.
  
  
  
  SNPhood is publicly available and maintained as an R Bioconductor package at http://bioconductor.org/packages/SNPhood/
  
  
  
  judith.zaugg@embl.de
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: European Molecular Biology Laboratory (EMBL), Heidelberg, 69117, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Arnold
authors.affiliation: European Molecular Biology Laboratory (EMBL), Heidelberg, 69117, Germany.
authors.forename: Pooja
authors.initials: P
authors.lastname: Bhat
authors.affiliation: European Molecular Biology Laboratory (EMBL), Heidelberg, 69117, Germany.
authors.forename: Judith B
authors.initials: JB
authors.lastname: Zaugg
mesh_terms: D057890:Epigenomics; D016678:Genome; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D012045:Regulatory Sequences, Nucleic Acid; D012984:Software