SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap

By Andrew D. Johnson, Robert E. Handsaker, S. Pulit, Marcia M. Nizzari, C. O’Donnell, P. D. Bakker. Bioinform., 2008

1,464 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/80ff8a1603192dfeb7665c28ebd9bd682cf4907b

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Molecular Biology

Citations in the corpus

Strong Protective Effect of The Aldehyde Dehydrogenase Gene (ALDH2) 504lys (*2) Allele Against Alcoholism And Alcohol-Induced Medical Diseases in Asians (2011, methodology): “In addition, the genotype data from the 1000 Genomes Project were also used to calculate and build the LD block (Johnson et al. 2008).”
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture (2013, positive): “7) and within 500kb of our best associating variant using SNAP.(2) We then used Annovar(108) to annotate these variants for functional effects based on RefSeq annotations.”
Systematic Evaluation of Pleiotropy Identifies 6 Further Loci Associated With Coronary Artery Disease (2017, positive): “For all associations, we identified the lead variant for that trait or disease and calculated pairwise LD with the lead CAD-associated variant using the SNAP web server (16).”
Impacts of Neanderthal-introgressed sequences on the landscape of human gene expression (2017, neutral): “…package Rue et al., 2009 http://www.r-inla.org SNAP Proxy Search Johnson et al., 2008 http://archive.broadinstitute.org/mpg/snap/ldsearch.php SIFT Kumar et al., 2009 http://sift.jcvi.org PolyPhen2 Adzhubei et al.,…”
Genome-Wide Association Study of Retinopathy in Individuals without Diabetes (2013, neutral): “2 [45].”
Multiple New Loci Associated with Kidney Function and Chronic Kidney Disease: The CKDGen consortium (2010, neutral): “The extent of LD between eSNPs below the correction threshold and the lead GWAS SNPs in the corresponding region was examined in the HapMap CEU population using SNA”
Genome-wide association study of blood pressure and hypertension (2009, methodology): “Plots of association results across each of the genome-wide significant loci are presented in Figures 1 and 2 using the SNAP too”
Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47 (2011, methodology): “764-S2">Supplementary Table 3 ; region-wide association plots (created using SNA”
Developmental regulation of human cortex transcription and its clinical relevance at base resolution (2014, positive): “For each list of rs numbers, we used the SNAP tool 71 to find all SNPs with R 2 > 0.6 in Caucasian 1000 Genomes samples (mirroring the summary statistics from the schizophrenia associations), and then created a linkage disequilibrium-based loci for each index SNP.”
Gene-Wide Analysis Detects Two New Susceptibility Genes for Alzheimer's Disease (2014, methodology): “92, calculated with SNAP software[20], 1000 genomes Pilot 1 dataset, CEU population panel, (http://www.”
HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants (2011, methodology): “To this end, HaploReg combines the focus on haplotype blocks provided by tools such as SNAP and SNPinfo with the breadth of genomic annotation provided by the full-featured genome browsers.”
Genomics to systems biology in animal and veterinary sciences: Progress, lessons and opportunities☆ (2014, methodology): “So with the knowledge of systems genetics of these genetic variants (and with tools such as FunctSNP, postGWAS, SNAP), one can categorize SNPs as functionally relevant and not relevant (residual genome).”