SNP FAQ Archive

This book contains actual questions asked by dbSNP and dbMHC users. We have tried to compile questions and answers that are representative of the entire spectrum of questions that our users ask, regardless of whether or not they are frequently asked. It is therefore likely that the question you have now, or a variant of it, may have been asked before, and may be in this book. The book will be updated with new questions regularly.

The questions and their answers have been edited for clarity and to protect the privacy of our users.

If you have a question about the SNP FAQ archive, or have a question you would like to see included in the archive, please contact vog.hin.mln.ibcn@nimda-pns

Contents

• dbSNP Submission Quick Start
  Created: April 6, 2007; Last Update: February 24, 2014.
  • Beginning the Submission Process
    Created: April 6, 2007; Last Update: February 24, 2014.
    • Creating/Using a Handle
  • Choosing a Submission Format
    Created: April 6, 2007; Last Update: February 24, 2014.
  • VCF Submissions
    Created: April 6, 2007; Last Update: February 24, 2014.
    • Using the VCF Excel Submission Template to create a Submission
    • VCF: Reporting Variant Positions
    • VCF: Reporting Variant Position and Resulting Submitted SNP (ss) and Reference SNP (rs) ID Assignment
  • Flat File Submissions
    Created: April 6, 2007; Last Update: February 24, 2014.
    • Documentation Required for a Flat File Submission
    • Choosing which Flat File Excel Submission Template(s) to Use
    • Using the Excel Submission Templates and Creating a Submission
  • Submitting Data and Submission Processing
    Created: April 6, 2007; Last Update: February 24, 2014.
    • Publication Issues
    • Data Types that can be Submitted to dbSNP
    • Using your Handle to Find your Assigned ss Numbers in dbSNP
• Searching dbSNP for Variations and Variation Data
  Created: July 7, 2005; Last Update: February 25, 2014.
  • General dbSNP Search Options
    Created: July 7, 2005; Last Update: February 25, 2014.
    • Introduction to Searching dbSNP
    • Using the Search Filter Options
    • Direct Database Queries
    • Entrez SNP
    • Search using a List of dbSNP ID Numbers
    • bioMart Type Search Function
  • Locating and Analyzing SNPs Associated with Disease Causing Mutations
    Created: July 7, 2005; Last Update: February 25, 2014.
    • dbSNP Locus Specific Database (LSDB)/Clinical Resources
    • Locating SNPs Associated with Disease Causing Mutations
    • Analysis of SNP Data Associated with a Specific Disease
  • Locating SNPs in a Gene or in Genes
    Created: July 7, 2005; Last Update: February 25, 2014.
    • Locating SNPs in a Specific Gene
    • Locating SNPs in a Gene in a Graphical Format
    • Locating a SNP in a Gene Using a Gene Name
    • Locating SNPs in a Named Gene
    • Locating a Specific Variation Type in a Named Gene
    • Locating a SNP in a Gene using an Amino Acid Variation
    • Locating SNPs in Specific Regions within a Gene
    • Locating SNPs in Multiple Copy Genes
    • Locating SNPs in Genes from a Specific Population
    • Locating Genes that Contain a Large Number of SNPs
    • Locating SNP Information for a Large Number of Genes
    • Locating SNPs in Promoters
    • Locating SNPs in Exons/Introns
    • Locating Exon Start/End positions
    • Locating SNPs in Stop Codons
    • Locating SNPs in Intergenic Regions
  • Locating SNPs in (a) Chromosome(s)
    Created: July 7, 2005; Last Update: February 25, 2014.
    • Finding SNPs in Specific Chromosome Regions
    • Finding SNPs using a Map of a Specific Chromosome Region
    • Finding SNPs that hit in Multiple Locations
    • Finding a Report Containing Chromosome/Physical Positions for each rs
    • Using Entrez to Find SNPs in a Chromosome
    • Using a List of refSNP(rs) Numbers to get a List of Chromosome Positions
    • Finding Chromosomal Coordinates for a SNP
    • Finding Chromosome Positions of Microsatellite Markers
    • Identification of Y Chromosome Specific SNPs
  • Locating ENCODE (Encyclopedia Of DNA Elements) Project SNPs
    Created: July 7, 2005; Last Update: February 25, 2014.
  • Locating SNPs in a Protein Family
    Created: July 7, 2005; Last Update: February 25, 2014.
  • Searching for SNP Primer Sequences
    Created: July 7, 2005; Last Update: February 25, 2014.
    • Commercial Primer Synthesis Firms
  • Searching for SNPs in a NCBI Genome Build and in BAC Clones
    Created: July 7, 2005; Last Update: February 25, 2014.
    • Searching for SNPs contained in the NCBI Genome Build
    • Searching for SNPs in BAC Clones
  • Searching for a Class of Variations in dbSNP
    Created: July 7, 2005; Last Update: February 25, 2014.
    • Searching for indels in dbSNP
  • Searching for SNPs or Specific SNP Data Using a Specific ID
    Created: July 7, 2005; Last Update: February 25, 2014.
    • Locating SNPs using Affymetrix IDs
    • Locating SNPs using Celera IDs
    • Locating SNPs using HGVS Recommended Nomenclature
    • Locating SNPs using Seattle SNPs IDs
    • Locating SNPs using STS IDs
    • Locating SNPs using PubMed ID
    • Locating SNPs using CGAP IDs
    • Locating SNPs using BAC Clone IDs
    • Locating Specific Data Using RefSNP(rs) or Submitted SNP(ss) ID
    • Locating SNPs using IDs Published in the Literature
  • Using SNP IDs to Find Genbank Accessions, and Vice Versa
    Created: July 7, 2005; Last Update: February 25, 2014.
  • Searching for SNPs Using Key Words, Names (Gene, Author, etc.), or Citations
    Created: July 7, 2005; Last Update: February 25, 2014.
    • Finding SNPs cited in PubMed
    • Finding SNPs using an Organism Name
    • Finding SNPs using a Gene Name
    • Finding SNPs using a Mutation Name
    • Finding SNPs Using a Key Word
    • Finding SNPs using a Submitter’s Name
  • Searching for SNPs Using Positional Data or EST Alignments
    Created: July 7, 2005; Last Update: February 25, 2014.
    • Searching for SNPs Using Positional Data
    • Searching for SNPs Using EST Alignments
  • Retrieving Specific Data for a SNP
    Created: July 7, 2005; Last Update: February 25, 2014.
    • Finding Contact Information for an Individual Submitter
    • Finding out which SNPs are Repeated and which have Multiple Submissions
    • Finding SNP Citations (SNP Publication Details)
    • Finding a Gene Name associated with a refSNP (rs) number
    • Finding Gene IDs associated with a refSNP (rs) number
    • Finding the Genetic Position of a SNP
    • Finding Strain Information for Submitted SNPs
    • Finding CpG Island Data
    • Finding Flanking Sequence Data
    • Finding SNPs that Lead to Premature Stop Codons
    • Finding Proximal (Neighboring) SNPs
    • Finding Wildtype Amino Acid
    • Finding Functional (Synonymous/Non-synonymous, etc.) Information for a SNP
    • Finding Hardy Weinburg Probabilities
    • Finding Hap-Tagged SNPs
    • Finding Specific Hetrerozygosity Data
    • Finding Orientation Data
    • Finding Organism Ploidy
    • Finding Records with OMIM Data/Links
    • Finding Reference Alleles
    • Finding Records for a Race or Specific Population
    • Finding Sample Size Data
    • Finding Tab-Delimited Reports
    • Finding Validation Data
    • Finding out why a SNP has been Withdrawn
  • Searching for SNP Genotype, Allele and Frequency Data
    Created: July 7, 2005; Last Update: February 25, 2014.
    • Searching for SNP Genotype Data
    • Searching for SNP Allele Data
    • Searching for SNP Frequency Data
  • Batch Query: Retrieving information for a large numbers of SNPs
    Created: July 7, 2005; Last Update: February 25, 2014.
    • Conducting BATCH Queries using Specific ID Types
    • Retrieving Specific Data using BATCH Query
    • BATCH Reports
    • BATCH Query Limits
    • BATCH Query Errors
  • Searching dbSNP using Sequence Data Homology (Search using BLAST)
    Created: July 7, 2005; Last Update: February 25, 2014.
    • Basic BLAST Search Strategies
    • Search dbSNP using a Sequence
    • BLASTing a Batch of Sequences
    • Searching dbSNP using Primer Sequence
    • Searching for SNPs not yet Submitted to dbSNP
    • Unable to get Sequence Comparison Results
    • Looking for SNP BLAST URL that Includes pre-set Parameters
  • Searching for SNPs in Raw Sequence Data
    Created: July 7, 2005; Last Update: February 25, 2014.
  • Searching for SNPs between Mouse Strains
    Created: July 7, 2005; Last Update: February 25, 2014.
  • Searching for Statistics, Data Histories and Historical Data in dbSNP
    Created: July 7, 2005; Last Update: February 25, 2014.
    • Searching for dbSNP Statistics
    • Searching for Data Histories and Historical Data
    • Finding a Build Number Based on a Date and Vice Versa
    • Searching for SNP Entry Dates for Patent Purposes
  • Searching for Structural (Copy Number) Variations
    Created: July 7, 2005; Last Update: February 25, 2014.
  • eSearch (Programmatic Searches)
    Created: July 7, 2005; Last Update: February 25, 2014.
    • Discrepancies Between Esearch Results and Direct SQL Queries
  • Search Result Discrepancies
    Created: July 7, 2005; Last Update: February 25, 2014.
    • Discrepancies between Web-based Search and Local Copy Search
    • Discrepancies between Web-based Search and SeqView Search
    • Discrepancies between dbSNP and ENSEMBL Searches
  • Errors that Occur While Searching
    Created: July 7, 2005; Last Update: February 25, 2014.
    • Unable to Find an rs Number
    • Unable to find SNPs for Specific Organism
    • Errors using Specific Search Terms
    • Errors using Specific Search Filters
    • Errors Searching with rs or ss Numbers
    • Runtime Error Message while Using Entrez SNP
    • Errors using Entrez Batch upload
  • Unable to Find Published SNP in dbSNP
    Created: July 7, 2005; Last Update: February 25, 2014.
• Submitting Variations and Variation Data to dbSNP
  Created: June 6, 2005; Last Update: June 15, 2010.
  • Submission Handles
    Created: June 6, 2005; Last Update: June 15, 2010.
    • Requesting a Handle
    • Handle Naming Convention
    • Changing Contact Information for a Handle
    • Handle Case Sensitivity
    • Requesting a Handle for Partners within a Consortium
    • Handle belongs to PI or PhD Student?
    • Submitting under an Existing Handle
    • Handles and Multiple Submitters
  • Requirements for dbSNP Submissions
    Created: June 6, 2005; Last Update: June 15, 2010.
    • GenBank Accession Numbers
  • Organism Data Accepted by dbSNP
    Created: June 6, 2005; Last Update: June 15, 2010.
  • Submitting Various Data Types to dbSNP
    Created: June 6, 2005; Last Update: June 15, 2010.
    • Mutation Submissions
    • Negative Data Submissions
    • Reporting Alleles
    • Genotype Submissions
    • Frequency Data Submissions
    • Microsatellite Data Submissions
    • Structural Variant Data Submissions
    • Submission of Multiple Linked SNPs
    • Submission of Data Found Using Various Methods
    • Submission of Previously Published SNPs
  • The dbSNP Excel Submission Template
    Created: June 6, 2005; Last Update: June 15, 2010.
  • Filling out the Submission Worksheets
    Created: June 6, 2005; Last Update: June 15, 2010.
    • Which Worksheet to Use
    • General Instructions for all Three Worksheets
    • Submitting Additional Information
    • The SNPASSAY Worksheet
    • The SNPINDUSE Worksheet
    • The SNPPOPUSE Worksheet
  • Filling out Specific Sections/Fields within a Submission Worksheet
    Created: June 6, 2005; Last Update: June 15, 2010.
    • The ACCESSION field
    • The SNP_ID field
    • The POPULATION section
    • The POP: ID field
    • The METHOD_CLASS field
    • The Method: ID field
    • The BATCH field
    • The PUBLICATION section
    • The SAMPLESIZE field
    • 5’_ASSAY and 3’_ASSAY fields
    • 5’_FLANK and 3’_FLANK fields
  • Submission Formatting
    Created: June 6, 2005; Last Update: June 15, 2010.
    • General Format Information for Submission
    • Sequence Formatting
    • Allele Formatting
    • Formatting Submissions of Specific Data Types
  • Automating the Submission Process
    Created: June 6, 2005; Last Update: June 15, 2010.
  • Submitting Information for Existing SNPs
    Created: June 6, 2005; Last Update: June 15, 2010.
    • Submitting Variations that already exist in dbSNP
    • Annotating existing SNPs
  • Batch Submissions and Large Submissions to dbSNP
    Created: June 6, 2005; Last Update: June 15, 2010.
  • Submitting SNPs using a Reference Sequence Position
    Created: June 6, 2005; Last Update: June 15, 2010.
  • Submission and Assignment of Submitted SNP(ss)/RefSNP(rs) Numbers
    Created: June 6, 2005; Last Update: June 15, 2010.
    • Submitted SNP (ss) Numbers
    • Reference SNP (rs) Number
    • Searching for SNPs Prior to refSNP (rs) number Assignment
  • dbSNP Submission Processing and the “Hold Until Published” (HUP) Policy
    Created: June 6, 2005; Last Update: June 15, 2010.
  • Submission Errors and Submission Withdrawal
    Created: June 6, 2005; Last Update: June 15, 2010.
    • Withdrawing Data from dbSNP
    • Fixing Errors in Submitted Data
    • Renaming SNPs
    • Why Specific RefSNPs have been withdrawn/deleted from dbSNP
  • Submission Using dbSNP’s online Clinical/LSDB Submission Resources
    Created: June 6, 2005; Last Update: June 15, 2010.
    • Submission using the Human Variation: Search, Annotate, Submit Site
    • Submission using the Variation Batch Submission Site
  • External Submission Tools
    Created: June 6, 2005; Last Update: June 15, 2010.
• Using dbSNP Data Reports
  Created: July 7, 2005; Last Update: February 18, 2014.
  • Entrez SNP and Entrez Gene Response Pages
    Created: July 7, 2005; Last Update: February 18, 2014.
  • Choosing the Data Report that Contains the Data You Need
    Created: July 7, 2005; Last Update: February 18, 2014.
  • Finding Information in a dbSNP Data Report
    Created: July 7, 2005; Last Update: February 18, 2014.
    • Entrez SNP Graphic Summary of Search
    • refSNP (rs) Cluster Reports
    • Submitted SNP (ss) Detail Reports
    • VarView
    • ASN.1. Reports
    • Chromosome Reports
    • FASTA Reports
    • FLATFILE Reports
    • Genotype Reports
    • XML Reports
  • Compact SNP data: The Bitfield
    Created: July 7, 2005; Last Update: February 18, 2014.
  • Custom Report Formats
    Created: July 7, 2005; Last Update: February 18, 2014.
  • Interpreting Discrepancies in refSNP Reports
    Created: July 7, 2005; Last Update: February 18, 2014.
    • The “Created/Updated” Field
    • Allele section
    • The Submitter Records Section
    • Geneview Section
    • Integrated Maps Section
    • Population Diversity Section (Frequency data)
    • Validation Summary Section
  • Interpreting Discrepancies in Submitted SNP (ss) Detail Reports
    Created: July 7, 2005; Last Update: February 18, 2014.
  • Discrepancies between Cluster Report Data and FTP Content
    Created: July 7, 2005; Last Update: February 18, 2014.
  • Discrepancies between Cluster Report data and Other Genome Resources
    Created: July 7, 2005; Last Update: February 18, 2014.
  • Field Definitions
    Created: July 7, 2005; Last Update: February 18, 2014.
  • SNP Class Definitions
    Created: July 7, 2005; Last Update: February 18, 2014.
    • Functional Class
    • Variation Class
  • Sequence Formatting in dbSNP Reports
    Created: July 7, 2005; Last Update: February 18, 2014.
    • Sequence Orientation
    • IUPAC Code
    • Lowercase (Small) Sequence Lettering
    • dbSNP 0-based (zero based) vs. 1-based Coordinate Representation
    • Flanking Sequence
  • Batch Reports
    Created: July 7, 2005; Last Update: February 18, 2014.
  • Displaying Reports
    Created: July 7, 2005; Last Update: February 18, 2014.
  • Links from dbSNP Reports to Other Online Data Resources
    Created: July 7, 2005; Last Update: February 18, 2014.
    • Links to SNP3D Structure Mapping
    • Links to OMIM
    • Links to GenBank
    • Links to TaqMan Assays
  • Links from Other Online Data Resources to dbSNP Reports
    Created: July 7, 2005; Last Update: February 18, 2014.
  • Creating Your Own Link to a dbSNP Record
    Created: July 7, 2005; Last Update: February 18, 2014.
  • Error Messages in refSNP Cluster Reports
    Created: July 7, 2005; Last Update: February 18, 2014.
• The dbSNP Build Process
  Created: July 7, 2005; Last Update: February 18, 2014.
  • What Triggers a New Build?
    Created: July 7, 2005; Last Update: February 18, 2014.
  • The SNP Build Schedule/Notification of Build Release
    Created: July 7, 2005; Last Update: February 18, 2014.
  • Data Changes that Occur Between Builds
    Created: July 7, 2005; Last Update: February 18, 2014.
    • New dbSNP Builds and Subsequent Changes to SNP Data
    • New Genome Builds and Subsequent Changes to Linked NCBI Resources
  • Lag Time between dbSNP Website and FTP Site Following Build
    Created: July 7, 2005; Last Update: February 18, 2014.
  • The Difference Between the SNP Build and the Genome Build
    Created: July 7, 2005; Last Update: February 18, 2014.
  • Using Old vs. New Build Data
    Created: July 7, 2005; Last Update: February 18, 2014.
  • Finding Old Build Data
    Created: July 7, 2005; Last Update: February 18, 2014.
  • Finding a Build Number Based on a Date and Vice Versa
    Created: July 7, 2005; Last Update: February 18, 2014.
  • The dbSNP Mapping Process
    Created: July 7, 2005; Last Update: February 18, 2014.
    • Mapping Weight
    • How dbSNP Determines SNP Positions
    • Chromosome Position and Contig Position
    • Locate Disappearing RefSNP (rs) Numbers
    • RefSNP (rs) Clusters Not Merging as Expected
    • Definition of loctype values
    • Reassigning loctype
    • Forward vs. Reverse strand Orientation
    • Sequence Notation for Variations
    • Position Notation for Variations
    • Mapping Discrepancies
  • Merging RefSNP Numbers and RefSNP Clusters
    Created: July 7, 2005; Last Update: February 18, 2014.
  • Ancestral Allele Data
    Created: July 7, 2005; Last Update: February 18, 2014.
    • Determining Ancestral Alleles
    • Annotating Ancestral Alleles
    • Interpreting Ancestral Allele Field in refSNP Report
  • Average Allele Frequency Calculation
    Created: July 7, 2005; Last Update: February 18, 2014.
  • Double Hit SNP Computation
    Created: July 7, 2005; Last Update: February 18, 2014.
  • Hardy Weinberg Equilibrium Data
    Created: July 7, 2005; Last Update: February 18, 2014.
  • Heterozygosity Data
    Created: July 7, 2005; Last Update: February 18, 2014.
  • Linkage Disequilibrium Data
    Created: July 7, 2005; Last Update: February 18, 2014.
  • dbSNP Haplotype Data
    Created: July 7, 2005; Last Update: February 18, 2014.
  • dbSNP and Haplogroup Data
    Created: July 7, 2005; Last Update: February 18, 2014.
  • dbSNP and Haplotype Tagged SNPs
    Created: July 7, 2005; Last Update: February 18, 2014.
  • dbSNP and HapMap Data
    Created: July 7, 2005; Last Update: February 18, 2014.
    • HapMap Genotype Discrepancies
• Locating and Using Data from dbSNP’s FTP Site
  Created: July 7, 2005; Last Update: February 18, 2014.
  • Navigating in dbSNP’s FTP Site
    Created: July 7, 2005; Last Update: February 18, 2014.
    • FTP Site Organization
    • FTP Site Documentation (Docsum)
  • Finding Specific Data in dbSNP’s FTP Files
    Created: July 7, 2005; Last Update: February 18, 2014.
    • Finding Functional Class Data
    • Finding Population Diversity Data
    • Finding IDs
    • Finding Mapping Data
    • Finding Sequence Data in CSV Format
    • Finding Microarray Data
    • Finding Merged RefSNP (rs) Data
    • Finding Deleted (no longer used) refSNP Numbers
    • Finding Method Data
    • Finding SNP data for NCBI Genome Builds
    • Finding Submitter Data
    • Finding Submitter Referenced Genbank Accessions
    • Finding Validation Data
    • Finding Variation Class Data
    • Finding SNPs for a Specific Organism
  • SNP Report Files
    Created: July 7, 2005; Last Update: February 18, 2014.
    • dbSNP FTP Site Report Formats
    • FTP File Descriptions and Definitions
    • Field Definitions
    • Specific File Location
    • Report Formats Not Available on dbSNP’s FTP Site
  • dbSNP Data Dictionary
    Created: July 7, 2005; Last Update: February 18, 2014.
  • Missing FTP Files
    Created: July 7, 2005; Last Update: February 18, 2014.
  • Downloading From dbSNP’s FTP Site
    Created: July 7, 2005; Last Update: February 18, 2014.
    • Problems Downloading
  • Decompressing Data Obtained from dbSNP’s FTP Site
    Created: July 7, 2005; Last Update: February 18, 2014.
  • Parsing Data Obtained from dbSNP’s FTP Site
    Created: July 7, 2005; Last Update: February 18, 2014.
    • Parsing Problems
  • Discrepancies between dbSNP Summary Data and FTP Data
    Created: July 7, 2005; Last Update: February 18, 2014.
  • Discrepancies between Cluster Report Data and FTP Data Contents
    Created: July 7, 2005; Last Update: February 18, 2014.
  • Discrepancies between FTP Documentation and Data Dictionary
    Created: July 7, 2005; Last Update: February 18, 2014.
  • Direct Queries of dbSNP’s Database Server
    Created: July 7, 2005; Last Update: February 18, 2014.
  • Updating dbSNP’s FTP data
    Created: July 7, 2005; Last Update: February 18, 2014.
  • Eutils (E-utilities)
    Created: July 7, 2005; Last Update: February 18, 2014.
    • Using eutils to Obtain Specific SNP Information
    • Eutils Workshops and Tutorials
    • Eutils Online Documentation
    • Using Eutils to Find Specific Data
    • eFetch
    • eSearch
    • XML Format for eutils
• dbSNP Organization and Structure (Schema)
  Created: August 8, 2005; Last Update: June 15, 2010.
  • Locating Schema Tables that Contain Specific SNP Data
    Created: August 8, 2005; Last Update: June 15, 2010.
    • Double Hit Data Table
    • Functional (synonymous, non-synonymous, etc.)Data Table
    • Genotype Data Tables
    • Mapping Data Tables
    • Merged/Expired RefSNP (rs) Tables
    • Population Diversity Tables
    • Split RefSNP (rs) Table
    • STS Accession Data Table
    • Submission Data Tables
  • SchemaTable Definitions/Locations
    Created: August 8, 2005; Last Update: June 15, 2010.
    • AlleleFreqBySsPop
    • OmimVarLocusIdSNP table
    • Publication Table
    • SNPAlleleFreq
    • SNPContigLoc Table
    • SNPContigLocusId Table
    • SNPFunctionCode Table
    • SNPSubSNPLink Table
    • SubInd Table
  • Field Definitions
    Created: August 8, 2005; Last Update: June 15, 2010.
    • SNPAncestralAllele table
    • SNPChrPosOnRef
    • SNPContigLocusId table
    • SubInd table
  • Schema Changes and Updates
    Created: August 8, 2005; Last Update: June 15, 2010.
    • Table Updates
    • Discrepancies between Tables
    • Replaced or Retired Tables and fields
  • dbSNP Build Updates and Schema Changes
    Created: August 8, 2005; Last Update: June 15, 2010.
  • Downloading Specific Schema Tables
    Created: August 8, 2005; Last Update: June 15, 2010.
  • How does dbSNP draw the Schema Tables
    Created: August 8, 2005; Last Update: June 15, 2010.
  • Local Copies of dbSNP
    Created: August 8, 2005; Last Update: June 15, 2010.
    • Direct Dumps of dbSNP
    • Creating a Local Copy of dbSNP for the Beginner
    • Creating a Local Copy of dbSNP in Various Database Systems
    • Creating a Local Copy on Linux
    • Creating a Local Copy that Contains Specific SNP Data
    • Creating a Local Copy that has Specific Applications
    • Keeping Local Copies Updated
    • Problems Downloading Data for Local Copies
    • Using SQL to Extract Data
    • The NSE Tables
    • Searching Local Copies of dbSNP
    • Discrepancies between a Local Copy Search and a Web-based Search
    • Discrepancies between the Data Dictionary and FTP Documentation
• dbSNP Data Content Information
  Created: July 23, 2005; Last Update: February 18, 2014.
  • dbSNP Data Origins
    Created: July 23, 2005; Last Update: February 18, 2014.
    • Data Exchange/Data Synchronization with other SNP Databases/Resources
  • dbSNP Data Quality Control
    Created: July 23, 2005; Last Update: February 18, 2014.
  • dbSNP Data Statistics
    Created: July 23, 2005; Last Update: February 18, 2014.
    • Statistics on Total Number of dbSNP Variations
    • Calculations of Mean SNP Density
    • Total number of RefSNPs vs.Total Number of Submitted SNPs
    • Summary of Annotated dbSNP Entries
    • dbSNP Growth Rate Statistics
  • dbSNP Data Storage Information
    Created: July 23, 2005; Last Update: February 18, 2014.
  • Classes of Genetic Variation Included in dbSNP
    Created: July 23, 2005; Last Update: February 18, 2014.
  • Size of Genetic Variations Included in dbSNP
    Created: July 23, 2005; Last Update: February 18, 2014.
  • Sequence Notation for SNPs Housed in dbSNP
    Created: July 23, 2005; Last Update: February 18, 2014.
  • Submitted SNPs (ss) and Other Data Submitted to dbSNP
    Created: July 23, 2005; Last Update: February 18, 2014.
    • Submitted SNPs (ss) Defined
    • Submitted Sequence Data
    • Species Data included in dbSNP
    • Ethnic Data in dbSNP
    • Strain Data In dbSNP
    • Submitter Information
    • Submitter Documentation for SNPs
    • HapMap Data
    • Computationally Derived SNPs
    • Published Mutations in dbSNP?
    • Validation Data
    • Population Diversity Data
  • Clustered RefSNPs (rs) and Other Data Computed in House
    Created: July 23, 2005; Last Update: February 18, 2014.
    • RefSNPs (rs) Defined
    • RefSNP (rs) Characteristics
    • Hardy Weinberg Equilibrium Data
    • Merging RefSNP Numbers and RefSNP Clusters
  • Ancestral Allele Data
    Created: July 23, 2005; Last Update: February 18, 2014.
    • Determining Ancestral Alleles
    • Annotating Ancestral Alleles
    • Interpreting Ancestral Allele Field in refSNP Report
  • Association Studies
    Created: July 23, 2005; Last Update: February 18, 2014.
  • Ascertainment Bias
    Created: July 23, 2005; Last Update: February 18, 2014.
    • References
  • Automated SNP Collection (Data Mining)
    Created: July 23, 2005; Last Update: February 18, 2014.
  • Average Allele Frequency Calculation
    Created: July 23, 2005; Last Update: February 18, 2014.
  • Double Hit SNP Computation
    Created: July 23, 2005; Last Update: February 18, 2014.
  • Hardy Weinberg Equilibrium Data
    Created: July 23, 2005; Last Update: February 18, 2014.
  • Heterozygosity Data
    Created: July 23, 2005; Last Update: February 18, 2014.
  • Linkage Disequilibrium Data
    Created: July 23, 2005; Last Update: February 18, 2014.
  • References
    Created: July 23, 2005; Last Update: February 18, 2014.
• Citing dbSNP
  Created: July 7, 2005; Last Update: June 15, 2010.
  • Citing dbSNP in a Publication
    Created: July 7, 2005; Last Update: June 15, 2010.
  • dbSNP Creation Date Information
    Created: July 7, 2005; Last Update: June 15, 2010.
  • dbSNP Database Statistics
    Created: July 7, 2005; Last Update: June 15, 2010.
  • Using dbSNP data in a Locally Created Public Search Engine
    Created: July 7, 2005; Last Update: June 15, 2010.
  • Using Images from NCBI Sites
    Created: July 7, 2005; Last Update: June 15, 2010.
• General Information about dbSNP, Single Nucleotide Polymorphisims, and Genetics
  • General Information about dbSNP as a Database Resource
  • General information about Single Nucleotide Polymorphisms
  • Information about Haplotypes
  • dbSNP and Phenotype Records
  • STR Naming Convention
  • Evolution Questions
  • Pedigree Software
  • Personal Haplotype Questions
  • Personal SNP Screenings
  • Human Gene Nomenclature
• Human Variation Batch Submission Quick Start
  Created: April 9, 2008; Last Update: June 15, 2010.
  • Data Types Accepted in a Variation Batch Submission
    Created: April 9, 2008; Last Update: June 15, 2010.
  • Beginning the Submission Process
    Created: April 9, 2008; Last Update: June 15, 2010.
    • Creating/Using a Handle
    • Creating/Changing your Password
    • What Documentation do I fill out for a Variation Batch Submission?
  • Using the Excel Submission Template to create your Batch Submission
    Created: April 9, 2008; Last Update: June 15, 2010.
  • Submitting Data
    Created: April 9, 2008; Last Update: June 15, 2010.
  • Submission Processing
    Created: April 9, 2008; Last Update: June 15, 2010.
    • What happens following Submission?
    • Validation Failure
    • Load Failure
  • Variation ID Assignment
    Created: April 9, 2008; Last Update: June 15, 2010.
  • Hold Until Published (HUP) Policy
    Created: April 9, 2008; Last Update: June 15, 2010.
  • How do I Update Data I’ve already Submitted?
    Created: April 9, 2008; Last Update: June 15, 2010.
  • How do I find my variations after submission, but before rs number assignment?
    Created: April 9, 2008; Last Update: June 15, 2010.
• Genome Workbench SNP Tools (GST) Quick Start
  Created: April 23, 2008; Last Update: June 15, 2010.
  • GST Defined
    Created: April 23, 2008; Last Update: June 15, 2010.
  • GST Features
    Created: April 23, 2008; Last Update: June 15, 2010.
  • Using GST for the First Time
    Created: April 23, 2008; Last Update: June 15, 2010.
    • Downloading GST
    • Loading Data to GST
    • Finding Help using GST
  • Using Specific GST Features
    Created: April 23, 2008; Last Update: June 15, 2010.
    • The Graphical View
    • The SNP Table View
  • Using GST to Study Genome Wide Association (GWAS) Data
    Created: April 23, 2008; Last Update: June 15, 2010.
    • Loading GWAS Data to GST