snp annotation and proxy search tool snap (Broad Institute Inc)
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snp annotation and proxy search tool snap
Snp Annotation And Proxy Search Tool Snap, supplied by Broad Institute Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/snp+annotation+and+proxy+search+-+snap/snp+annotation+and+proxy+search/med_rxiv__2023__02__23__23286339-34-9-16
Average 90 stars, based on 1 article reviews
Snp Annotation And Proxy Search Tool Snap, supplied by Broad Institute Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/snp+annotation+and+proxy+search+-+snap/snp+annotation+and+proxy+search/med_rxiv__2023__02__23__23286339-34-9-16
Average 90 stars, based on 1 article reviews
snp annotation and proxy search tool snap - by Bioz Stars,
2026-10
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Variant Assay:Article Title: Genome-wide association studies and contribution to cardiovascular physiology Article Snippet: 1000 Genomes project, http://www.1000genomes.org SNP Annotation and Proxy Search - SNAP, http://www.broadinstitute.org/mpg/snap/ eQTL browser at NCBI, http://www.ncbi.nlm.nih.gov/projects/gap/eqtl/index.cgi GenVar at the Sanger Institute, http://www.sanger.ac.uk/resources/software/genevar/ Scan DB, http://www.scandb.org Broad Institute GTex Browser, http://www.gtexportal.org eQTL resources at the Prichard Lab, http://eqtl.uchicago.edu Encylopedia of DNA Elements - ENCODE, http://genome.ucsc.edu/ENCODE/ Roadmap Epigenomics Project, http://www.roadmapepigenomics.org HAPLOREG, http://www.broadinstitute.org/mammals/haploreg RegulomeDB, http://regulome.stanford.edu Exome chip, http://genome.sph.umich.edu/wiki/Exome_Chip_Design International Mouse Phenotyping Consortium http://www.mousephenotype.org/ Rat Genome Database, http://rgd.mcw.edu Zebrafish Mutation Project, http://www.sanger.ac.uk/Projects/D_rerio/zmp/ CHOPCHOP, https://chopchop.rc.fas.harvard.edu UK Biobank, http://www.ukbiobank.ac.uk/ Farr Institute, http://www.farrinstitute.org/ Article Title: Data integration for functional annotation of regulatory single nucleotide polymorphisms associated with Alzheimer's disease susceptibility. Article Snippet: Background: Alzheimer's disease (AD), the most common form of dementia affects 24.3 million people worldwide.. More than twenty genetic loci have been associated with AD and a significant number of genetic variants were mapped within these loci.. A large proportion of genome wide significant variants lie outside the coding region. Article Title: ABCG2 Regulatory SNPs Alter In Vivo Enhancer Activity and Expression Article Snippet: SNPs in linkage disequilibrium with rs12508471, rs72873421, rs149713212, rs9999111 and rs2725263 (r 2 threshold ≥ 0.8) were extracted from 1000 Genomes pilot 1 genotype data using the Broad Institute SNP annotation and proxy search (SNAP) version 2.2[ 18 ] for each population (CEU, YRI and CHB+JBT) separately and linkage analysis was performed using the Haploview program version 4.2[ 19 ] Variant Enhancer Plasmid Construction Reference enhancer plasmids in the pGL4.23 vector were previously described[ 15 ]. Article Title: Comparison of variation in frequency for SNPs associated with asthma or liver disease between Estonia, HapMap populations and the 1000 genome project populations. Article Snippet: Genome‐Wide Association Studies (GWAS) have identified an abun‐ dance of single nucleotide polymorphisms (SNPs) associated with disease phenotypes, but clinical understanding remains limited.. These discoveries provide important insights into the genetic archi‐ tecture of complex traits while also providing new opportunities to understand the biology of complex diseases.. Allele‐specific analyses to understand frequency differences between populations, partic‐ ularly populations not well studied, are important to help identify genetic variants that may have been affected by natural selection or which may have a functional effect on disease mechanisms and phenotypic predisposition, motivating new GWA studies in more di‐ verse populations around the world to enable novel genetic findings to aid the development of new therapies to reduce morbidity and mortality. Article Title: Dopaminergic and Opioid Pathways Associated with Impulse Control Disorders in Parkinson’s Disease Article Snippet: A further 12 single-nucleotide polymorphisms (SNPs) were removed based on a high linkage disequilibrium (LD) measured using the Broad Institute SNP Annotation and Proxy Search (SNAP) ( ). Article Title: Genomic risk prediction of aromatase inhibitor‐related arthralgia in patients with breast cancer using a novel machine‐learning algorithm Article Snippet: Article Title: An exploratory phenome wide association study linking asthma and liver disease genetic variants to electronic health records from the Estonian Biobank Article Snippet: Where primary SNPs of interest were not available on this array, the Broad Institute SNP Annotation and Proxy Search (SNAP) tool was used to identify proxy SNPs (SNPs which can represent the primary SNP of interest) with a minimum linkage disequilibrium r 2 ≥0.6 [ ]. Article Title: ABCG2 Regulatory SNPs Alter In Vivo Enhancer Activity and Expression Article Snippet: SNPs in linkage disequilibrium with rs12508471, rs72873421, rs149713212, rs9999111 and rs2725263 (r 2 threshold ≥ 0.8) were extracted from 1000 Genomes pilot 1 genotype data using the Broad Institute SNP annotation and proxy search (SNAP) version 2.2[ 18 ] for each population (CEU, YRI and CHB+JBT) separately and linkage analysis was performed using the Haploview program version 4.2[ 19 ] Plasmid Preparation:Article Title: Genome-wide association studies and contribution to cardiovascular physiology Article Snippet: 1000 Genomes project, http://www.1000genomes.org SNP Annotation and Proxy Search - SNAP, http://www.broadinstitute.org/mpg/snap/ eQTL browser at NCBI, http://www.ncbi.nlm.nih.gov/projects/gap/eqtl/index.cgi GenVar at the Sanger Institute, http://www.sanger.ac.uk/resources/software/genevar/ Scan DB, http://www.scandb.org Broad Institute GTex Browser, http://www.gtexportal.org eQTL resources at the Prichard Lab, http://eqtl.uchicago.edu Encylopedia of DNA Elements - ENCODE, http://genome.ucsc.edu/ENCODE/ Roadmap Epigenomics Project, http://www.roadmapepigenomics.org HAPLOREG, http://www.broadinstitute.org/mammals/haploreg RegulomeDB, http://regulome.stanford.edu Exome chip, http://genome.sph.umich.edu/wiki/Exome_Chip_Design International Mouse Phenotyping Consortium http://www.mousephenotype.org/ Rat Genome Database, http://rgd.mcw.edu Zebrafish Mutation Project, http://www.sanger.ac.uk/Projects/D_rerio/zmp/ CHOPCHOP, https://chopchop.rc.fas.harvard.edu UK Biobank, http://www.ukbiobank.ac.uk/ Farr Institute, http://www.farrinstitute.org/ Article Title: Data integration for functional annotation of regulatory single nucleotide polymorphisms associated with Alzheimer's disease susceptibility. Article Snippet: Background: Alzheimer's disease (AD), the most common form of dementia affects 24.3 million people worldwide.. More than twenty genetic loci have been associated with AD and a significant number of genetic variants were mapped within these loci.. A large proportion of genome wide significant variants lie outside the coding region. Article Title: ABCG2 Regulatory SNPs Alter In Vivo Enhancer Activity and Expression Article Snippet: SNPs in linkage disequilibrium with rs12508471, rs72873421, rs149713212, rs9999111 and rs2725263 (r 2 threshold ≥ 0.8) were extracted from 1000 Genomes pilot 1 genotype data using the Broad Institute SNP annotation and proxy search (SNAP) version 2.2[ 18 ] for each population (CEU, YRI and CHB+JBT) separately and linkage analysis was performed using the Haploview program version 4.2[ 19 ] Variant Enhancer Plasmid Construction Reference enhancer plasmids in the pGL4.23 vector were previously described[ 15 ]. Article Title: Comparison of variation in frequency for SNPs associated with asthma or liver disease between Estonia, HapMap populations and the 1000 genome project populations. Article Snippet: Genome‐Wide Association Studies (GWAS) have identified an abun‐ dance of single nucleotide polymorphisms (SNPs) associated with disease phenotypes, but clinical understanding remains limited.. These discoveries provide important insights into the genetic archi‐ tecture of complex traits while also providing new opportunities to understand the biology of complex diseases.. Allele‐specific analyses to understand frequency differences between populations, partic‐ ularly populations not well studied, are important to help identify genetic variants that may have been affected by natural selection or which may have a functional effect on disease mechanisms and phenotypic predisposition, motivating new GWA studies in more di‐ verse populations around the world to enable novel genetic findings to aid the development of new therapies to reduce morbidity and mortality. Article Title: Dopaminergic and Opioid Pathways Associated with Impulse Control Disorders in Parkinson’s Disease Article Snippet: A further 12 single-nucleotide polymorphisms (SNPs) were removed based on a high linkage disequilibrium (LD) measured using the Broad Institute SNP Annotation and Proxy Search (SNAP) ( ). Article Title: Genomic risk prediction of aromatase inhibitor‐related arthralgia in patients with breast cancer using a novel machine‐learning algorithm Article Snippet: Article Title: An exploratory phenome wide association study linking asthma and liver disease genetic variants to electronic health records from the Estonian Biobank Article Snippet: Where primary SNPs of interest were not available on this array, the Broad Institute SNP Annotation and Proxy Search (SNAP) tool was used to identify proxy SNPs (SNPs which can represent the primary SNP of interest) with a minimum linkage disequilibrium r 2 ≥0.6 [ ]. Article Title: ABCG2 Regulatory SNPs Alter In Vivo Enhancer Activity and Expression Article Snippet: SNPs in linkage disequilibrium with rs12508471, rs72873421, rs149713212, rs9999111 and rs2725263 (r 2 threshold ≥ 0.8) were extracted from 1000 Genomes pilot 1 genotype data using the Broad Institute SNP annotation and proxy search (SNAP) version 2.2[ 18 ] for each population (CEU, YRI and CHB+JBT) separately and linkage analysis was performed using the Haploview program version 4.2[ 19 ] Northern Blot:Article Title: Genome-wide association studies and contribution to cardiovascular physiology Article Snippet: 1000 Genomes project, http://www.1000genomes.org SNP Annotation and Proxy Search - SNAP, http://www.broadinstitute.org/mpg/snap/ eQTL browser at NCBI, http://www.ncbi.nlm.nih.gov/projects/gap/eqtl/index.cgi GenVar at the Sanger Institute, http://www.sanger.ac.uk/resources/software/genevar/ Scan DB, http://www.scandb.org Broad Institute GTex Browser, http://www.gtexportal.org eQTL resources at the Prichard Lab, http://eqtl.uchicago.edu Encylopedia of DNA Elements - ENCODE, http://genome.ucsc.edu/ENCODE/ Roadmap Epigenomics Project, http://www.roadmapepigenomics.org HAPLOREG, http://www.broadinstitute.org/mammals/haploreg RegulomeDB, http://regulome.stanford.edu Exome chip, http://genome.sph.umich.edu/wiki/Exome_Chip_Design International Mouse Phenotyping Consortium http://www.mousephenotype.org/ Rat Genome Database, http://rgd.mcw.edu Zebrafish Mutation Project, http://www.sanger.ac.uk/Projects/D_rerio/zmp/ CHOPCHOP, https://chopchop.rc.fas.harvard.edu UK Biobank, http://www.ukbiobank.ac.uk/ Farr Institute, http://www.farrinstitute.org/ Article Title: Data integration for functional annotation of regulatory single nucleotide polymorphisms associated with Alzheimer's disease susceptibility. Article Snippet: Background: Alzheimer's disease (AD), the most common form of dementia affects 24.3 million people worldwide.. More than twenty genetic loci have been associated with AD and a significant number of genetic variants were mapped within these loci.. A large proportion of genome wide significant variants lie outside the coding region. Article Title: ABCG2 Regulatory SNPs Alter In Vivo Enhancer Activity and Expression Article Snippet: SNPs in linkage disequilibrium with rs12508471, rs72873421, rs149713212, rs9999111 and rs2725263 (r 2 threshold ≥ 0.8) were extracted from 1000 Genomes pilot 1 genotype data using the Broad Institute SNP annotation and proxy search (SNAP) version 2.2[ 18 ] for each population (CEU, YRI and CHB+JBT) separately and linkage analysis was performed using the Haploview program version 4.2[ 19 ] Variant Enhancer Plasmid Construction Reference enhancer plasmids in the pGL4.23 vector were previously described[ 15 ]. Article Title: Comparison of variation in frequency for SNPs associated with asthma or liver disease between Estonia, HapMap populations and the 1000 genome project populations. Article Snippet: Genome‐Wide Association Studies (GWAS) have identified an abun‐ dance of single nucleotide polymorphisms (SNPs) associated with disease phenotypes, but clinical understanding remains limited.. These discoveries provide important insights into the genetic archi‐ tecture of complex traits while also providing new opportunities to understand the biology of complex diseases.. Allele‐specific analyses to understand frequency differences between populations, partic‐ ularly populations not well studied, are important to help identify genetic variants that may have been affected by natural selection or which may have a functional effect on disease mechanisms and phenotypic predisposition, motivating new GWA studies in more di‐ verse populations around the world to enable novel genetic findings to aid the development of new therapies to reduce morbidity and mortality. Article Title: Dopaminergic and Opioid Pathways Associated with Impulse Control Disorders in Parkinson’s Disease Article Snippet: A further 12 single-nucleotide polymorphisms (SNPs) were removed based on a high linkage disequilibrium (LD) measured using the Broad Institute SNP Annotation and Proxy Search (SNAP) ( ). Article Title: Genomic risk prediction of aromatase inhibitor‐related arthralgia in patients with breast cancer using a novel machine‐learning algorithm Article Snippet: Article Title: An exploratory phenome wide association study linking asthma and liver disease genetic variants to electronic health records from the Estonian Biobank Article Snippet: Where primary SNPs of interest were not available on this array, the Broad Institute SNP Annotation and Proxy Search (SNAP) tool was used to identify proxy SNPs (SNPs which can represent the primary SNP of interest) with a minimum linkage disequilibrium r 2 ≥0.6 [ ]. Article Title: ABCG2 Regulatory SNPs Alter In Vivo Enhancer Activity and Expression Article Snippet: SNPs in linkage disequilibrium with rs12508471, rs72873421, rs149713212, rs9999111 and rs2725263 (r 2 threshold ≥ 0.8) were extracted from 1000 Genomes pilot 1 genotype data using the Broad Institute SNP annotation and proxy search (SNAP) version 2.2[ 18 ] for each population (CEU, YRI and CHB+JBT) separately and linkage analysis was performed using the Haploview program version 4.2[ 19 ] Western Blot:Article Title: Genome-wide association studies and contribution to cardiovascular physiology Article Snippet: 1000 Genomes project, http://www.1000genomes.org SNP Annotation and Proxy Search - SNAP, http://www.broadinstitute.org/mpg/snap/ eQTL browser at NCBI, http://www.ncbi.nlm.nih.gov/projects/gap/eqtl/index.cgi GenVar at the Sanger Institute, http://www.sanger.ac.uk/resources/software/genevar/ Scan DB, http://www.scandb.org Broad Institute GTex Browser, http://www.gtexportal.org eQTL resources at the Prichard Lab, http://eqtl.uchicago.edu Encylopedia of DNA Elements - ENCODE, http://genome.ucsc.edu/ENCODE/ Roadmap Epigenomics Project, http://www.roadmapepigenomics.org HAPLOREG, http://www.broadinstitute.org/mammals/haploreg RegulomeDB, http://regulome.stanford.edu Exome chip, http://genome.sph.umich.edu/wiki/Exome_Chip_Design International Mouse Phenotyping Consortium http://www.mousephenotype.org/ Rat Genome Database, http://rgd.mcw.edu Zebrafish Mutation Project, http://www.sanger.ac.uk/Projects/D_rerio/zmp/ CHOPCHOP, https://chopchop.rc.fas.harvard.edu UK Biobank, http://www.ukbiobank.ac.uk/ Farr Institute, http://www.farrinstitute.org/ Article Title: Data integration for functional annotation of regulatory single nucleotide polymorphisms associated with Alzheimer's disease susceptibility. Article Snippet: Background: Alzheimer's disease (AD), the most common form of dementia affects 24.3 million people worldwide.. More than twenty genetic loci have been associated with AD and a significant number of genetic variants were mapped within these loci.. A large proportion of genome wide significant variants lie outside the coding region. Article Title: ABCG2 Regulatory SNPs Alter In Vivo Enhancer Activity and Expression Article Snippet: SNPs in linkage disequilibrium with rs12508471, rs72873421, rs149713212, rs9999111 and rs2725263 (r 2 threshold ≥ 0.8) were extracted from 1000 Genomes pilot 1 genotype data using the Broad Institute SNP annotation and proxy search (SNAP) version 2.2[ 18 ] for each population (CEU, YRI and CHB+JBT) separately and linkage analysis was performed using the Haploview program version 4.2[ 19 ] Variant Enhancer Plasmid Construction Reference enhancer plasmids in the pGL4.23 vector were previously described[ 15 ]. Article Title: Comparison of variation in frequency for SNPs associated with asthma or liver disease between Estonia, HapMap populations and the 1000 genome project populations. Article Snippet: Genome‐Wide Association Studies (GWAS) have identified an abun‐ dance of single nucleotide polymorphisms (SNPs) associated with disease phenotypes, but clinical understanding remains limited.. These discoveries provide important insights into the genetic archi‐ tecture of complex traits while also providing new opportunities to understand the biology of complex diseases.. Allele‐specific analyses to understand frequency differences between populations, partic‐ ularly populations not well studied, are important to help identify genetic variants that may have been affected by natural selection or which may have a functional effect on disease mechanisms and phenotypic predisposition, motivating new GWA studies in more di‐ verse populations around the world to enable novel genetic findings to aid the development of new therapies to reduce morbidity and mortality. Article Title: Dopaminergic and Opioid Pathways Associated with Impulse Control Disorders in Parkinson’s Disease Article Snippet: A further 12 single-nucleotide polymorphisms (SNPs) were removed based on a high linkage disequilibrium (LD) measured using the Broad Institute SNP Annotation and Proxy Search (SNAP) ( ). Article Title: Genomic risk prediction of aromatase inhibitor‐related arthralgia in patients with breast cancer using a novel machine‐learning algorithm Article Snippet: Article Title: An exploratory phenome wide association study linking asthma and liver disease genetic variants to electronic health records from the Estonian Biobank Article Snippet: Where primary SNPs of interest were not available on this array, the Broad Institute SNP Annotation and Proxy Search (SNAP) tool was used to identify proxy SNPs (SNPs which can represent the primary SNP of interest) with a minimum linkage disequilibrium r 2 ≥0.6 [ ]. Article Title: ABCG2 Regulatory SNPs Alter In Vivo Enhancer Activity and Expression Article Snippet: SNPs in linkage disequilibrium with rs12508471, rs72873421, rs149713212, rs9999111 and rs2725263 (r 2 threshold ≥ 0.8) were extracted from 1000 Genomes pilot 1 genotype data using the Broad Institute SNP annotation and proxy search (SNAP) version 2.2[ 18 ] for each population (CEU, YRI and CHB+JBT) separately and linkage analysis was performed using the Haploview program version 4.2[ 19 ] |