SNP cohort

Aliases

311,226 SNPs, 500,000 SNPs, >500K SNPs, G, GWS SNP, GWS lead SNP, OCD-associated SNP, PIP>0.95 SNPs, SNP, SNP allele dosage, SNP dataset, SNP effects, SNP genotype, SNP genotypes, SNP variation, SNP3, SNP3 locus, SNP3^G+, SNPs, Single Nucleotide Polymorphism, X, Xl, ancestry informative markers, autosomal SNP, autosomal SNPs, autosomal marker, best SNPs, common variants, control SNP, falsely-significant SNPs, four SNPs, functional SNP, genetic variant, genome wide significant SNPs, genome-wide SNPs, genotyped SNP, genotyped SNPs, given SNP, high-quality SNPs, implicated SNPs, imputed SNP dosages, independent SNPs, index SNP, individual SNPs, jth SNP, lead SNP, loci, marker, nominally-positive SNP, palindromic SNPs, pleiotropic SNPs, polymorphic SNP, polymorphism, poorly-imputed SNPs, proxy SNP, rare allele, remaining SNPs, risk marker, selected SNPs, single SNP, single nucleotide polymorphism, single nucleotide polymorphism markers, single nucleotide polymorphisms, single-nucleotide polymorphism, snip, specific SNPs, tagSNP, tagged SNP, two SNPs

Related entities (75)

Mentioned in (170)

Papers in which this entity is mentioned.

• Advancing regulatory variant effect prediction with AlphaGenome. (2026)
• Mapping the genetic landscape across 14 psychiatric disorders. (2026)
• Specificity, length and luck drive gene rankings in association studies. (2026)
• Modeling heterogeneity in single-cell perturbation states enhances detection of response eQTLs. (2025)
• Concordance between male- and female-specific GWAS results helps define underlying genetic architecture of complex traits. (2025)
• Massively parallel reporter assay investigates shared genetic variants of eight psychiatric disorders. (2025)
• Multiple overlapping binding sites determine transcription factor occupancy. (2025)
• Genome-wide association testing beyond SNPs. (2025)
• Genome-wide analyses identify 30 loci associated with obsessive-compulsive disorder. (2025)
• Nucleotide Transformer: building and evaluating robust foundation models for human genomics. (2025)
• KILDA: identifying KIV-2 repeats from kmers. (2025)
• Improving polygenic risk prediction in admixed populations by explicitly modeling ancestral-differential effects via GAUDI. (2024)
• BridgePRS leverages shared genetic effects across ancestries to increase polygenic risk score portability. (2024)
• MUSSEL: Enhanced Bayesian polygenic risk prediction leveraging information across multiple ancestry groups. (2024)
• Yield of genetic association signals from genomes, exomes and imputation in the UK Biobank. (2024)
• Integrative polygenic risk score improves the prediction accuracy of complex traits and diseases. (2024)
• Principles and methods for transferring polygenic risk scores across global populations. (2024)
• Global impact of unproductive splicing on human gene expression. (2024)
• Clinical, genomic, and neurophysiological correlates of lifetime suicide attempts among individuals with alcohol dependence. (2024)
• CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods. (2024)
• Detection and analysis of complex structural variation in human genomes across populations and in brains of donors with psychiatric disorders. (2024)
• Integrated Single-Cell Multiomic Profiling of Caudate Nucleus Suggests Key Mechanisms in Alcohol Use Disorder. (2024)
• Nanopore sequencing with unique molecular identifiers enables accurate mutation analysis and haplotyping in the complex lipoprotein(a) KIV-2 VNTR. (2024)
• Genome-wide association analyses identify 95 risk loci and provide insights into the neurobiology of post-traumatic stress disorder. (2024)
• A harmonized public resource of deeply sequenced diverse human genomes. (2024)
• Benchmarking short and long read polishing tools for nanopore assemblies: achieving near-perfect genomes for outbreak isolates. (2024)
• Biobank-scale methods and projections for sparse polygenic prediction from machine learning. (2023)
• Unsupervised discovery of ancestry-informative markers and genetic admixture proportions in biobank-scale datasets. (2023)
• Guidelines for Evaluating the Comparability of Down-Sampled GWAS Summary Statistics. (2023)
• Polygenic scoring accuracy varies across the genetic ancestry continuum. (2023)
• Genetic Influences on the Developing Young Brain and Risk for Neuropsychiatric Disorders. (2023)
• Multi-trait genome-wide association study of opioid addiction: OPRM1 and beyond. (2022)
• Single-cell analysis of somatic mutations in human bronchial epithelial cells in relation to aging and smoking. (2022)
• Genome-wide mutational signatures in low-coverage whole genome sequencing of cell-free DNA. (2022)
• Item-Level Genome-Wide Association Study of the Alcohol Use Disorders Identification Test in Three Population-Based Cohorts. (2022)
• Research Review: A guide to computing and implementing polygenic scores in developmental research. (2022)
• Human Retrotransposons and Effective Computational Detection Methods for Next-Generation Sequencing Data. (2022)
• Parsing genetically influenced risk pathways: genetic loci impact problematic alcohol use via externalizing and specific risk. (2022)
• Principal Component Analyses (PCA)-based findings in population genetic studies are highly biased and must be reevaluated. (2022)
• Inferring population structure in biobank-scale genomic data. (2022)
• Large-scale collaboration in ENIGMA-EEG: A perspective on the meta-analytic approach to link neurological and psychiatric liability genes to electrophysiological brain activity. (2021)
• Using a developmental perspective to examine the moderating effects of marriage on heavy episodic drinking in a young adult sample enriched for risk. (2021)
• Integrated Genomic Analysis Identifies Driver Genes and Cisplatin-Resistant Progenitor Phenotype in Pediatric Liver Cancer. (2021)
• Detecting cell-type-specific allelic expression imbalance by integrative analysis of bulk and single-cell RNA sequencing data. (2021)
• Integrative reconstruction of cancer genome karyotypes using InfoGenomeR. (2021)
• Multivariate analysis of 1.5 million people identifies genetic associations with traits related to self-regulation and addiction. (2021)
• Data structures based on -mers for querying large collections of sequencing data sets. (2021)
• Genetic association study of childhood aggression across raters, instruments, and age. (2021)
• Rapid genotype imputation from sequence with reference panels. (2021)
• Genotypes of informative loci from 1000 Genomes data allude evolution and mixing of human populations. (2021)
• Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. (2021)
• Predicting risk for Alcohol Use Disorder using longitudinal data with multimodal biomarkers and family history: a machine learning study. (2021)
• Sibling comparisons elucidate the associations between educational attainment polygenic scores and alcohol, nicotine and cannabis. (2020)
• GenMap: ultra-fast computation of genome mappability. (2020)
• Tutorial: a guide to performing polygenic risk score analyses. (2020)
• ASEP: Gene-based detection of allele-specific expression across individuals in a population by RNA sequencing. (2020)
• Cancer PRSweb: An Online Repository with Polygenic Risk Scores for Major Cancer Traits and Their Evaluation in Two Independent Biobanks. (2020)
• Accucopy: Accurate and Fast Inference of Allele-specific Copy Number Alterations from Low-coverage Low-purity Tumor Sequencing Data (2020)
• Detecting cell-type-specific allelic expression imbalance by integrative analysis of bulk and single-cell RNA sequencing data (2020)
• Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. (2020)
• Genome-wide meta-analysis of problematic alcohol use in 435,563 individuals yields insights into biology and relationships with other traits. (2020)
• Polygenic prediction via Bayesian regression and continuous shrinkage priors. (2019)
• Exploring the relationship between polygenic risk for cannabis use, peer cannabis use and the longitudinal course of cannabis involvement. (2019)
• Ploidy- and Purity-Adjusted Allele-Specific DNA Analysis Using CLONETv2. (2019)
• Interrogating the Genetic Determinants of Tourette's Syndrome and Other Tic Disorders Through Genome-Wide Association Studies. (2019)
• Linking genes, circuits, and behavior: network connectivity as a novel endophenotype of externalizing. (2019)
• Integrating predicted transcriptome from multiple tissues improves association detection. (2019)
• CYP2A6 is associated with obesity: studies in human samples and a high fat diet mouse model. (2019)
• The mutational constraint spectrum quantified from variation in 141,456 humans (2019)
• Integrating predicted transcriptome from multiple tissues improves association detection. (2019)
• Genome-wide association study of alcohol consumption and use disorder in 274,424 individuals from multiple populations. (2019)
• VCF2CNA: A tool for efficiently detecting copy-number alterations in VCF genotype data and tumor purity. (2019)
• Ethanol activates immune response in lymphoblastoid cells. (2019)
• A multi-task convolutional deep neural network for variant calling in single molecule sequencing. (2019)
• Genome-wide association analyses of risk tolerance and risky behaviors in over 1 million individuals identify hundreds of loci and shared genetic influences. (2019)
• Genome-wide association analysis links multiple psychiatric liability genes to oscillatory brain activity. (2018)
• Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing. (2018)
• A SNP panel for identification of DNA and RNA specimens. (2018)
• Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. (2018)
• Enter the Matrix: Factorization Uncovers Knowledge from Omics. (2018)
• Comprehensive Characterization of Cancer Driver Genes and Mutations. (2018)
• A compendium of conserved cleavage and polyadenylation events in mammalian genes. (2018)
• Meta-Analysis of Genetic Influences on Initial Alcohol Sensitivity. (2018)
• Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. (2018)
• The Immune Landscape of Cancer. (2018)
• Nanopore sequencing and assembly of a human genome with ultra-long reads. (2018)
• PASSPORT-seq: A Novel High-Throughput Bioassay to Functionally Test Polymorphisms in Micro-RNA Target Sites. (2018)
• The fractured landscape of RNA-seq alignment: the default in our STARs. (2018)
• Annotation-free quantification of RNA splicing using LeafCutter. (2018)
• A Brief Critique of the TATES Procedure. (2018)
• The Impact of Peer Substance Use and Polygenic Risk on Trajectories of Heavy Episodic Drinking Across Adolescence and Emerging Adulthood. (2017)
• ChimeRScope: a novel alignment-free algorithm for fusion transcript prediction using paired-end RNA-Seq data. (2017)
• Genetic correlates of the development of theta event related oscillations in adolescents and young adults. (2017)
• The fractured landscape of RNA-seq alignment: The default in our STARs (2017)
• ReMixT: clone-specific genomic structure estimation in cancer. (2017)
• Fast and Accurate Genomic Analyses using Genome Graphs (2017)
• Eigenanalysis of SNP data with an identity by descent interpretation. (2016)
• KAT2B polymorphism identified for drug abuse in African Americans with regulatory links to drug abuse pathways in human prefrontal cortex. (2016)
• GeneiASE: Detection of condition-dependent and static allele-specific expression from RNA-seq data without haplotype information. (2016)
• Reference-based phasing using the Haplotype Reference Consortium panel. (2016)
• ascatNgs: Identifying Somatically Acquired Copy-Number Alterations from Whole-Genome Sequencing Data. (2016)
• Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer. (2016)
• FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing. (2016)
• Detecting Genomic Signatures of Natural Selection with Principal Component Analysis: Application to the 1000 Genomes Data. (2016)
• Polygenic risk for alcohol dependence associates with alcohol consumption, cognitive function and social deprivation in a population-based cohort. (2016)
• The PsychENCODE project. (2015)
• Tools and best practices for data processing in allelic expression analysis. (2015)
• Recurrent somatic mutations in regulatory regions of human cancer genomes. (2015)
• A gene-based association method for mapping traits using reference transcriptome data. (2015)
• Peroxisome proliferator-activated receptors α and γ are linked with alcohol consumption in mice and withdrawal and dependence in humans. (2015)
• A global reference for human genetic variation. (2015)
• Candidate gene-environment interaction research: reflections and recommendations. (2015)
• Design and bioinformatics analysis of genome-wide CLIP experiments. (2015)
• The landscape of long noncoding RNAs in the human transcriptome. (2015)
• Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data. (2015)
• Genome-wide association study of nicotine dependence in American populations: identification of novel risk loci in both African-Americans and European-Americans. (2015)
• WASP: allele-specific software for robust molecular quantitative trait locus discovery. (2015)
• HLA-VBSeq: accurate HLA typing at full resolution from whole-genome sequencing data. (2015)
• MBASED: allele-specific expression detection in cancer tissues and cell lines. (2014)
• Unraveling the clonal hierarchy of somatic genomic aberrations. (2014)
• Hidden Markov Model-Based CNV Detection Algorithms for Illumina Genotyping Microarrays. (2014)
• RADIA: RNA and DNA integrated analysis for somatic mutation detection. (2014)
• RNA-binding protein RBM20 represses splicing to orchestrate cardiac pre-mRNA processing. (2014)
• Genome-wide association study of cocaine dependence and related traits: FAM53B identified as a risk gene. (2014)
• Transcriptome sequencing of a large human family identifies the impact of rare noncoding variants. (2014)
• VariantDB: a flexible annotation and filtering portal for next generation sequencing data. (2014)
• An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. (2014)
• TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data. (2014)
• Diminishing return for increased Mappability with longer sequencing reads: implications of the k-mer distributions in the human genome. (2014)
• Using genetic information from candidate gene and genome-wide association studies in risk prediction for alcohol dependence. (2014)
• Common biological networks underlie genetic risk for alcoholism in African- and European-American populations. (2013)
• A genome-wide association study of alcohol-dependence symptom counts in extended pedigrees identifies C15orf53. (2013)
• A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks. (2013)
• QualComp: a new lossy compressor for quality scores based on rate distortion theory. (2013)
• ACMG clinical laboratory standards for next-generation sequencing. (2013)
• Pdgfra protects against ethanol-induced craniofacial defects in a zebrafish model of FASD. (2013)
• Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. (2013)
• Dosage transmission disequilibrium test (dTDT) for linkage and association detection. (2013)
• The Genotype-Tissue Expression (GTEx) project. (2013)
• Characterizing and measuring bias in sequence data. (2013)
• Landscape of transcription in human cells. (2012)
• The aggregate effect of dopamine genes on dependence symptoms among cocaine users: cross-validation of a candidate system scoring approach. (2012)
• Amyloid pathway-based candidate gene analysis of [(11)C]PiB-PET in the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort. (2012)
• Copy number variations in 6q14.1 and 5q13.2 are associated with alcohol dependence. (2012)
• cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate. (2012)
• A cross-sample statistical model for SNP detection in short-read sequencing data. (2012)
• Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. (2012)
• Fast computation and applications of genome mappability. (2012)
• An integrated encyclopedia of DNA elements in the human genome. (2012)
• GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. (2011)
• Linkage analysis merging replicate phenotypes: an application to three quantitative phenotypes in two African samples. (2011)
• A framework for variation discovery and genotyping using next-generation DNA sequencing data. (2011)
• Genome-wide association study of theta band event-related oscillations identifies serotonin receptor gene HTR7 influencing risk of alcohol dependence. (2011)
• Genomic regions identified by overlapping clusters of nominally-positive SNPs from genome-wide studies of alcohol and illegal substance dependence. (2011)
• Allele-specific copy number analysis of tumors. (2010)
• Integrative analysis of the melanoma transcriptome. (2010)
• Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. (2010)
• A new statistic to evaluate imputation reliability. (2010)
• TumorBoost: normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays. (2010)
• Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. (2010)
• Evidence for genes on chromosome 2 contributing to alcohol dependence with conduct disorder and suicide attempts. (2010)
• Genomic copy number determination in cancer cells from single nucleotide polymorphism microarrays based on quantitative genotyping corrected for aneuploidy. (2009)
• Recurring mutations found by sequencing an acute myeloid leukemia genome. (2009)
• Fast and accurate short read alignment with Burrows-Wheeler transform. (2009)
• VarScan: variant detection in massively parallel sequencing of individual and pooled samples. (2009)
• Fewer permutations, more accurate P-values. (2009)
• Copy-number-variation and copy-number-alteration region detection by cumulative plots. (2009)
• Rapid SNP discovery and genetic mapping using sequenced RAD markers. (2008)
• PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. (2007)
• A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC. (2006)

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