I assume you want human build 125 and 126 map positions, right? You could get them in the organism_data subdirectory for each organism (the link above goes to the human organism_data subdirectory). Please Note: the files you are looking for start with the build number followed by “SNPContigLoc”; e.g. b125_SNPContigLoc_35_1. The column definitions for SNPContigLoc are located in dbSNP’s Database Dictionary. (03/07/08)

You can use dbSNP Batch Query service to download the Flat File Report format for a list of rs numbers. The Flat File Report contains chromosome, chromosome position, and allele information for each refSNP. You may also wish to look at the ancestral allele section of the SNP FAQ archive for further information on ancestral alleles. (9/19/06)

On the Batch query submission page select "Chromosome Report" as the result format. (4/10/06)

1.

Go to the dbSNP home page, and scroll down to the “Batch” section.

2.

In the “upload list” sub-section, select “Reference SNP ID (rs)”.

3.

On the data request form, enter the email address where you want your data sent, select the organism of interest from the “organism” dropdown menu, and in the “Select Result Format” section choose “CHROMOSOME RPT” from the dropdown menu (3/1/06).

You can upload your list of refSNP numbers (30,000/per load) to the batch query service and request the “FLATFILE” report.

Click this link to see the FLATFILE report for rs1855025. (5/12/05)

Frequency information is located in the genotype report. Please use the batch query and select genotypeReport.

Create a list using only the local SNP ID, but don't include the handle.

Batch Query currently only works for those SNPs that have been clustered into a RefSNP (rs), even though you are only asking for a submitted SNP (ss) report. We understand that this is a problem when there is a substantial lag time between the ss submission and rs clustering. In December of 2008 we instituted a new Batch Query feature that allows a Batch Query search for pre-clustering ss fasta reports. (10/09/08)

You can use dbSNP Batch Query Service to download the FASTA format for a list of rs numbers. (9/19/06)

The Batch query is not the correct way to proceed. Instead, you will have to write a program using the eutils programming utilities:

1.

Use eSearch to perform the search, and then parse out the refSNP (rs) numbers you need. Here are the results for a search for SNPs in the human LPL gene.

2.

Use eFetch to retrieve the SNP reports (6/20/06)

dbSNP doesn't have a BATCH query for Gene ID. You’ll have to use eSearch and eFetch to do it programmatically. There is another FAQ in this archive that shows you how use eSearch and eFetch in this way. (5/22/08)

Use the following instructions to upload the ss numbers of interest using the Batch query service and request the Submitted SNP “SubSNP” details report format:

1.

Go to dbSNP Batch Query page.

2.

Scroll down to the submission format drop-down menu and select “Upload SS#”.

3.

Enter your email address in the appropriate text box, and select the organism of interest from the organism drop-down menu.

4.

Select "SubSNP Details" from the Result Format drop-down menu.

5.

Upload the series of ss numbers of interest using the “Browse” button. Once you have uploaded the ss numbers, Click on the “Submit” button.

The Batch query limit is 30,000 SS numbers per request. (4/4/06)

When you are entering your BATCH query, select the chromosome report as your result format. The chromosome report format is a tab-delimited table that can be imported into Excel. You’ll have to use efetch to get the allele frequency from the XML files (FREQXML), however. Remember that NOT all SNPs have frequency data. Examples of the different dbSNP formats retrieved using efetch located online. (7/28/06)

I would recommend that you use an XML parser because of the complex structure of XML. There are parsers available for most common computer languages. You can see an example of parsers used in PERL. Another option is to use XSLT to extract and transform XML to the format of your choice.

To get the rs allele frequency directly, use the FTP file, SNPAlleleFreq.bcp.gz, located in your organism’s organism_data directory (ex: human).

The fields in the file are tab delimited and are defined in the schema table for your organism (ex: human).

Here are instructions for obtaining an genotype exchange XML file for a set of specific SNPs:

If you have a list of SNPs (rs numbers), you can upload the list to batch query by using the rs page. At the rs page, type in your email address. Then select genotypeReport as the format and click on submit. The report will be emailed to you.

Alternatively, if you want a large list of rs numbers and want to start from a Entrez query, do the following:

Once you have narrowed your Entrez query to the list that you want, select the dbSNP Batch report option, click display, and follow the instructions in the rs list example.

In addition to the SNP-specific queries, we are currently exploring various options for allowing users to specify population, pedigree, and/or individual filters as limits to the downloads for the genotype exchange XML report.

The flanking sequences will be from the current build — dbSNP build 125, which is based on human genome build 36.(5/10/06)

Try using the non-Entrez Batch query service and requesting the genotype xml report which include allele frequency. We'll look into the generating a simpler frequency report. (03/26/08)

The file you're trying to access was created in 2003 and has been deleted from the system. We cannot keep files in the FTP site for than 48 hours because of limited resources. Please submit your query again to generate a new file.

The batch query service only dumps reports for SNPs that have been clustered and assigned with reference SNP (rs) numbers. The pig SNPs you are inquiring about have yet to be clustered and assigned with reference SNP (rs) numbers.

The batch query does not work for unclustered SNPs, and since the records you submitted represent submitted SNPs (ss) that were not mapped and/or clustered, you did not receive a response. You can download the records for these SNPs from the dbSNP FTP site.

(7/18/06)

Only submitted SNPs that have had refSNP (rs) numbers assigned to them can be as can be released in the FLATFILE or XML report formats. The submitted SNP (ss) numbers you submitted for a Batch query were only just recently assigned to some new submissions that came into dbSNP, and therefore have not been assigned refSNP (rs) numbers yet. The rs numbers will be assigned by the next dbSNP release. (3/29/06)

Make sure that the file you upload contains one SNP per line with the submitter handle and Local SNP ID delimited with a pipe “|” (e.g. TSC-CSHL|TSC0000026).

Also, please note that the maximum upload for each file is 30K IDs or lines. The query will fail if you exceed this limit.(10/06/08)

You can use dbSNP’s Entrez batch query system if you're querying with refSNP (rs) numbers. The Entrez SNP batch query system is fast, but it can accept only rs numbers, and as such you need only submit the number without the “rs” prefix attached.

1.

Go to the SNP batch Entrez page

2.

Click on the "Browse" button at the top of the page, and select the rs list you intend to query.

3.

Click on the "Retrieve" button located next to the “Browse” button

4.

When the result is shown, select the “Display” option and select a report from the list of available report types.

5.

Select the “Send to” option to save or print the report.(5/19/06)