{"entity": "publication", "iuid": "3ab84aea084e4f65ae0c022fdf121f46", "timestamp": "2020-05-28T15:21:32.405Z", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3ab84aea084e4f65ae0c022fdf121f46.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3ab84aea084e4f65ae0c022fdf121f46"}}, "title": "Allele-specific transcription factor binding in liver and cervix cells unveils many likely drivers of GWAS signals.", "authors": [{"family": "Cavalli", "given": "Marco", "initials": "M"}, {"family": "Pan", "given": "Gang", "initials": "G"}, {"family": "Nord", "given": "Helena", "initials": "H"}, {"family": "Wall\u00e9n Arzt", "given": "Emelie", "initials": "E"}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Wadelius", "given": "Claes", "initials": "C"}], "type": "journal article", "published": "2016-06-00", "journal": {"volume": "107", "issn": "1089-8646", "issue": "6", "pages": "248-254", "title": "Genomics"}, "abstract": "Genome-wide association studies (GWAS) point to regions with associated genetic variants but rarely to a specific gene and therefore detailed knowledge regarding the genes contributing to complex traits and diseases remains elusive. The functional role of GWAS-SNPs is also affected by linkage disequilibrium with many variants on the same haplotype and sometimes in the same regulatory element almost equally likely to mediate the effect. Using ChIP-seq data on many transcription factors, we pinpointed genetic variants in HepG2 and HeLa-S3 cell lines which show a genome-wide significant difference in binding between alleles. We identified a collection of 3713 candidate functional regulatory variants many of which are likely drivers of GWAS signals or genetic difference in expression. A recent study investigated many variants before finding the functional ones at the GALNT2 locus, which we found in our genome-wide screen in HepG2. This illustrates the efficiency of our approach.", "doi": "10.1016/j.ygeno.2016.04.006", "pmid": "27126307", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Compute and Storage": "Service"}, "xrefs": [{"db": "pii", "key": "S0888-7543(16)30027-1"}], "notes": null, "qc": null, "created": "2017-05-08T07:57:21.629Z", "modified": "2020-01-21T13:56:06.826Z"}