DOI: 10.6084/m9.figshare.871430.v3
title: SNPsea: an algorithm to identify cell types, tissues, and pathways affected by risk loci

description: February 12, 2014 This archive contains data for: <em>SNPsea: an algorithm to identify cell types, tissues, and pathways that affect risk loci</em> Please see the SNPsea documentation for more details: http://www.broadinstitute.org/mpg/snpsea <strong>Celiac_disease-Trynka2011-35_SNPs.gwas</strong> 35 SNPs associated with Celiac disease taken from Table 2.<br>Positions are on hg19. All SNPs have P &lt;= 5e-8. doi:10.1038/ng.998<br>PMID: 22057235 Trynka G, Hunt KA, Bockett NA, et al. <em>Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease.</em> Nat Genet. 2011;43(12):1193-201. http://www.ncbi.nlm.nih.gov/pubmed/22057235 <strong>HDL_cholesterol-Tesolvich2010-46_SNPs.gwas</strong> 46 SNPs associated with HDL taken from Supplementary Table 2.<br>Positions are on hg19. All SNPs have P &lt;= 5e-8. doi:10.1038/nature09270<br>PMID: 20686565 Teslovich TM, Musunuru K, Smith AV, et al. <em>Biological, clinical and population relevance of 95 loci for blood lipids.</em> Nature. 2010;466(7307):707-13. http://www.ncbi.nlm.nih.gov/pubmed/20686565 <strong>Multiple_sclerosis-IMSGC-51_SNPs.gwas</strong> 51 SNPs associated with Multiple Sclerosis taken from Supplementary Table A.<br>Positions are on hg19. All SNPs have P &lt;= 5e-8. doi:10.1038/nature10251<br>PMID: 21833088 Sawcer S, Hellenthal G, Pirinen M, et al. <em>Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.</em> Nature. 2011;476(7359):214-9. http://www.ncbi.nlm.nih.gov/pubmed/21833088 <strong>Red_blood_cell_count-Harst2012-45_SNPs.gwas</strong> 45 SNPs associated with red blood cell count (RBC) taken from Table 1. Positions are on hg19. All SNPs have P &lt;= 5e-8. doi:10.1038/nature11677<br>PMID: 23222517 Van der harst P, Zhang W, Mateo leach I, et al. <em>Seventy-five genetic loci influencing the human red blood cell.</em> Nature. 2012;492(7429):369-75. http://www.ncbi.nlm.nih.gov/pubmed/23222517 - - - <strong>GeneAtlas2004.gct.gz</strong> Gene expression data for 79 human tissues from GSE1133. Replicates for each tissue profile were averaged. For each gene, the single probe with the largest minimum was selected. Su AI et al. <em>A gene atlas of the mouse and human protein-encoding transcriptomes.</em> Proc Natl Acad Sci U S A, 2004 Apr 9;101(16):6062-7 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1133 <strong>GO2013.gct.gz</strong> A GCT formatted gene matrix with 1s and 0s indicating presence or absence of<br>genes in Gene Ontology annotations. http://www.geneontology.org/ <strong>ImmGen2012.gct.gz</strong> Gene expression data for 249 blood cell types from GSE15907. Replicates for each cell type profile were averaged. For each gene, the single probe with the largest minimum was selected. Immunological Genome Project http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15907 - - - <strong>NCBIgenes2013.bed.gz</strong> All human gene start and stop positions taken from: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2refseq.gz <strong>Lango2010.txt.gz</strong> A list of SNPs that span the whole genome, pruned by linkage disequilibrium (LD). SNPsea samples null SNP sets matched on the number of genes in the user's SNP set from this list. See this paper for more information: Lango allen H, Estrada K, Lettre G, et al. <em>Hundreds of variants clustered in genomic loci and biological pathways affect human height.</em> Nature. 2010;467(7317):832-8. http://www.ncbi.nlm.nih.gov/pubmed/20881960 <strong>TGP2011.bed.gz</strong> Linkage intervals for a filtered set of SNPs from the 1000 Genomes Project Phase 1 (May 21, 2011). SNP genotypes were obtained from the BEAGLE release v3 website and processed to create linkage intervals for each SNP. The linkage intervals were extended to the nearest HapMap recombination hotspot with &gt;3 cM/Mb recombination rate. http://www.1000genomes.org/<br>http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes.phase1_release_v3/<br>http://hapmap.ncbi.nlm.nih.gov/downloads/