NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.
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 StartCreated: April 6, 2007; Last Update: February 24, 2014.
- Searching dbSNP for Variations and Variation DataCreated: July 7, 2005; Last Update: February 25, 2014.
- General dbSNP Search Options
- Locating and Analyzing SNPs Associated with Disease Causing Mutations
- Locating SNPs in a Gene or in Genes
- 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)
- 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
- Locating SNPs in a Protein Family
- Searching for SNP Primer Sequences
- Searching for SNPs in a NCBI Genome Build and in BAC Clones
- Searching for a Class of Variations in dbSNP
- Searching for SNPs or Specific SNP Data Using a Specific ID
- 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
- Searching for SNPs Using Key Words, Names (Gene, Author, etc.), or Citations
- Searching for SNPs Using Positional Data or EST Alignments
- Retrieving Specific Data for a SNP
- 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
- Batch Query: Retrieving information for a large numbers of SNPs
- Searching dbSNP using Sequence Data Homology (Search using BLAST)
- Searching for SNPs in Raw Sequence Data
- Searching for SNPs between Mouse Strains
- Searching for Statistics, Data Histories and Historical Data in dbSNP
- Searching for Structural (Copy Number) Variations
- eSearch (Programmatic Searches)
- Search Result Discrepancies
- Errors that Occur While Searching
- Unable to Find Published SNP in dbSNP
- Submitting Variations and Variation Data to dbSNPCreated: June 6, 2005; Last Update: June 15, 2010.
- Submission Handles
- Requirements for dbSNP Submissions
- Organism Data Accepted by dbSNP
- Submitting Various Data Types to dbSNP
- The dbSNP Excel Submission Template
- Filling out the Submission Worksheets
- Filling out Specific Sections/Fields within a Submission Worksheet
- Submission Formatting
- Automating the Submission Process
- Submitting Information for Existing SNPs
- Batch Submissions and Large Submissions to dbSNP
- Submitting SNPs using a Reference Sequence Position
- Submission and Assignment of Submitted SNP(ss)/RefSNP(rs) Numbers
- dbSNP Submission Processing and the “Hold Until Published” (HUP) Policy
- Submission Errors and Submission Withdrawal
- Submission Using dbSNP’s online Clinical/LSDB Submission Resources
- External Submission Tools
- Using dbSNP Data ReportsCreated: July 7, 2005; Last Update: February 18, 2014.
- Entrez SNP and Entrez Gene Response Pages
- Choosing the Data Report that Contains the Data You Need
- Finding Information in a dbSNP Data Report
- Compact SNP data: The Bitfield
- Custom Report Formats
- Interpreting Discrepancies in refSNP Reports
- Interpreting Discrepancies in Submitted SNP (ss) Detail Reports
- Discrepancies between Cluster Report Data and FTP Content
- Discrepancies between Cluster Report data and Other Genome Resources
- Field Definitions
- SNP Class Definitions
- Sequence Formatting in dbSNP Reports
- Batch Reports
- Displaying Reports
- Links from dbSNP Reports to Other Online Data Resources
- Links from Other Online Data Resources to dbSNP Reports
- Creating Your Own Link to a dbSNP Record
- Error Messages in refSNP Cluster Reports
- The dbSNP Build ProcessCreated: July 7, 2005; Last Update: February 18, 2014.
- What Triggers a New Build?
- The SNP Build Schedule/Notification of Build Release
- Data Changes that Occur Between Builds
- Lag Time between dbSNP Website and FTP Site Following Build
- The Difference Between the SNP Build and the Genome Build
- Using Old vs. New Build Data
- Finding Old Build Data
- Finding a Build Number Based on a Date and Vice Versa
- The dbSNP Mapping Process
- 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
- Ancestral Allele Data
- Average Allele Frequency Calculation
- Double Hit SNP Computation
- Hardy Weinberg Equilibrium Data
- Heterozygosity Data
- Linkage Disequilibrium Data
- dbSNP Haplotype Data
- dbSNP and Haplogroup Data
- dbSNP and Haplotype Tagged SNPs
- dbSNP and HapMap Data
- Locating and Using Data from dbSNP’s FTP SiteCreated: July 7, 2005; Last Update: February 18, 2014.
- Finding Specific Data in dbSNP’s FTP Files
- 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
- dbSNP Data Dictionary
- Missing FTP Files
- Downloading From dbSNP’s FTP Site
- Decompressing Data Obtained from dbSNP’s FTP Site
- Parsing Data Obtained from dbSNP’s FTP Site
- Discrepancies between dbSNP Summary Data and FTP Data
- Discrepancies between Cluster Report Data and FTP Data Contents
- Discrepancies between FTP Documentation and Data Dictionary
- Direct Queries of dbSNP’s Database Server
- Updating dbSNP’s FTP data
- Eutils (E-utilities)
- Finding Specific Data in dbSNP’s FTP Files
- dbSNP Organization and Structure (Schema)Created: August 8, 2005; Last Update: June 15, 2010.
- Locating Schema Tables that Contain Specific SNP Data
- SchemaTable Definitions/Locations
- Field Definitions
- Schema Changes and Updates
- dbSNP Build Updates and Schema Changes
- Downloading Specific Schema Tables
- How does dbSNP draw the Schema Tables
- Local Copies of dbSNP
- 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 InformationCreated: July 23, 2005; Last Update: February 18, 2014.
- dbSNP Data Origins
- dbSNP Data Quality Control
- dbSNP Data Statistics
- dbSNP Data Storage Information
- Classes of Genetic Variation Included in dbSNP
- Size of Genetic Variations Included in dbSNP
- Sequence Notation for SNPs Housed in dbSNP
- Submitted SNPs (ss) and Other Data Submitted to dbSNP
- Clustered RefSNPs (rs) and Other Data Computed in House
- Ancestral Allele Data
- Association Studies
- Ascertainment Bias
- Automated SNP Collection (Data Mining)
- Average Allele Frequency Calculation
- Double Hit SNP Computation
- Hardy Weinberg Equilibrium Data
- Heterozygosity Data
- Linkage Disequilibrium Data
- References
- Citing dbSNPCreated: July 7, 2005; Last Update: June 15, 2010.
- General Information about dbSNP, Single Nucleotide Polymorphisims, and Genetics
- Human Variation Batch Submission Quick StartCreated: April 9, 2008; Last Update: June 15, 2010.
- Data Types Accepted in a Variation Batch Submission
- Beginning the Submission Process
- Using the Excel Submission Template to create your Batch Submission
- Submitting Data
- Submission Processing
- Variation ID Assignment
- Hold Until Published (HUP) Policy
- How do I Update Data I’ve already Submitted?
- How do I find my variations after submission, but before rs number assignment?
- Genome Workbench SNP Tools (GST) Quick StartCreated: April 23, 2008; Last Update: June 15, 2010.