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SNP FAQ Archive [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2005-.

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SNP FAQ Archive [Internet].

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Submission and Assignment of Submitted SNP(ss)/RefSNP(rs) Numbers

Submitted SNP (ss) Numbers

ss Number Maintenance

Will a SNP keep its submitted SNP (ss) number once it has been assigned a refSNP (rs) number, or is the ss number no longer used?

A good explanation of the relationship between refSNPs (rs#) and Submitted SNPs (ss#) can be found in the "Computed Content" section of the dbSNP Handbook. Look in the "Submitted SNPs and Reference SNP Clusters" subsection. For more information regarding the assignment of rs numbers and citing unclustered ss numbers in a publication, look in the “Do I Need a RefSNP Number for Publication” sub section of this dbSNP FAQ archive (submission) section. (9/12/07)

How long does it take to get a Submitted SNP (ss) Number

Can you tell me how long it will take to receive a dbSNP number after I submit data to dbSNP?

It should take between one and two weeks to get a submitted SNP (ss) number. Your submission may be delayed if it requires correction or if it was submitted before a major holiday. RefSNP ID numbers (rs#) are assigned at a later time since they represent a cluster of submitted SNPs that map to the same contig. (3/11/05)

Finding a SNP after ss number assignment, but before rs number assignment

I submitted a batch of SNPs a while ago and got the ss numbers for the SNPs, but I’m unable to find them when I search the dbSNP website.

Follow the steps below to see your submitted SNPs:

1.

Go to the dbSNP home page and locate the “Submission Information” section.

2.

Locate the link “By Submitter” in the “Submitter Information” section — it is the first selection — and click on it. You will go to the “Search/View Submitter Detail” page.

3.

Type your Handle into the empty text box on the page, make sure the radio buttons for “Submitter Handle” and “Starts With” are selected, and click the “Search” button. For this example, I will use the Handle “KWOK”.

4.

Once you press “Search” in the previous step, the “Search/View Submitter Detail” page will refresh to include a list of handles.

5.

Click on your handle (in this example, KWOK), which will take you to the SNP Submitter Contact Detail page, which will have a list of the batches you submitted.

6.

Click on the blue link for the Batch ID you are interested in to see your data. For this example I selected KWOK’s Assay link, 10.23.98, and was sent to the “View Submission Batch” page for this batch, where you can see all the data submitted in this batch.

(01/31/08)

How do I find my ss Numbers using my Handle?

I submitted SNPs some time ago, and all is well, but I’m unable to find a list of my submitted SNPs. How do I do this using my Handle?

You can find the submitted SNP numbers assigned to your submissions by following these steps:

1.

Go to the dbSNP Home page

2.

Go to the “Submission Information” section and click on the first link in the section: “By Submitter”, which will take you to the “Search/View Submitter Detail” page

3.

Type your Handle (I used OMIMSNP) into the text box, make sure the radio buttons for “Submitter handle” and “Starts with” have been selected, and click the “Search” button.

4.

The “Search/View Submitter Detail” page will refresh, showing a table of handles at the bottom.

5.

Click on your handle (located on the far right in the handle column (for this example I will click on OMIMSNP), which will take you to the “Submitter Contact Detail” page.

6.

On the the “Submitter Contact Detail” page, click on the “Submitter Batch ID” of interest (in this case there is only one), to go to the “View SNP Submission Batch” page, where all the submitted SNP (ss) numbers assigned to the SNPs submitted in that particular batch are listed.

(01/23/08)

Reference SNP (rs) Number

How are RefSNP Numbers Assigned?

How do I avoid redundant RefSNP (rs) numbers when submitting data?

We map each new submission to the most recent genome assembly. If a new submitted SNP (ss) maps to the same position as an existing RefSNP (rs), then the new ss will be assigned the existing rs number. If the new ss and the old rs both have identical mapping positions, you do not need to do anything special to avoid redundant rs numbers. But, when a new ss does not map to any contig, we assign a new rs number to this ss. (5/17/05)

We observed two different SNPs at the same position, T/T and C/T, where the reference sequence is C/C. Would these two alleles be assigned individual refSNP numbers, or would they be assigned one refSNP number together?

We cluster submitted SNPs into a refSNP based on the submitted SNPs’ genome mapping position, or based on their flanking sequence similarity. In your case, the two SNPs you found would be assigned one refSNP ID number. To report alleles in a submitted SNP, you would list all the alleles that you have observed in a mapping position. In your case, it would be “C” and “T”, so you would report the SNP as “C/T”. If you have individual sample genotypes, then you would report the genotype for each individual.

We have SNPs obtained from various sources that we would like to submit, but we are unable to map them onto refSNPs. Why?

An rs number can change. Here is why: A unique rs number is a cluster of all ss numbers positioned on the same place in the genome assembly. With each new build, we often find that previously separate rs numbers are actually in the same place. So we merge them (see an example of such a merge). If you use the rs exemplar, which is the ss number with the longest flanking sequence in the cluster, it is easier for you to track your submission data in the future because the ss number is much more stable. It is only in rare cases that a submitter will withdraw a submission.

How long does it take to get a refSNP (rs) Number?

How long does it take to get a RefSNP ID number when I submit a SNP? I need it for a manuscript.

As soon as we load your SNP submission file into our database, you will get a submitted SNP ID number (ss#), which you can put in your manuscript. Please let us know when you need the ss# and we will try to get your SNP loaded by the date specified.

Can you tell me how long it will take to receive a dbSNP number after I submit data to dbSNP?

It should take between one and two weeks to get a submitted SNP (ss) number. Your submission may be delayed if it requires correction or if it was submitted before a major holiday. RefSNP ID numbers (rs#) are assigned at a later time since they represent a cluster of submitted SNPs that map to the same contig. (3/11/05)

Do I Need a RefSNP Number for Publication?

I submitted two SNPs six months ago and can find the submitted SNP (ss) numbers on dbSNP, but not the refSNP (rs) numbers. The SNPs are going to be published in a month and I want to include the rs numbers in the text.

These submitted SNPs should be clustered and assigned rs numbers in dbSNP build 127, which should be out in a few weeks.

You should, however, be using the submitted SNP (ss) numbers to cite the SNPs in your paper since they're unique to your submission. A refSNP number can change between builds if the genome changes, so citing the refSNP number in your publication could possibly mislead users wanting to access your SNPs in the future. A user can always use dbSNP’s “Search by ID” feature on the dbSNP home page to find the corresponding refSNP (rs) number for the ss number you cite in your publication. Please review the following dbSNP FAQ sections from the dbSNP FAQ archive for further information:

RefSNPs (rs) Defined

Citing dbSNP in a Publication

(12/15/06)

How do I check for rs Number Assignment

I’ve submitted millions of mouse SNPs, and have their submitted (ss) numbers — how do I check to see if they have refSNP (rs) numbers yet?

You can use BATCH query to search for a large number of submitted SNPs, but please note that BATCH query does not work for unclustered SNPs, so those SNPs in your list that have yet to be clustered will not show up on the report.

Your rs assignments should be released in the next build if your SNPs were submitted before the data freeze. If you subscribe to the dbSNP announcements mailing list, you will be notified as to the release date of the next build. For questions about BATCH queries, look in the BATCH query section of the dbSNP archive; specifically, the section entitled “Unable to Access Recently Submitted SNPs using BATCH”. Also, look in submission section of the archive in the sub-section entitled “Searching for SNPs Prior to refSNP (rs) number Assignment” (9/12/07)

Interpreting Unexpected rs Number Data

I recently received rs numbers for my 144 submitted SNPs — 5 of these SNPs had “N.D.” in the "chr" and "contig_accession" columns. What does “N.D.” mean?

“N.D.” in this case means that the SNP didn't map by BLAST analysis to the chromosome or contig. (05/15/08)

Searching for SNPs Prior to refSNP (rs) number Assignment

I submitted a batch of SNPs a while ago and got the ss numbers for the SNPs, but I’m unable to find them when I search the dbSNP website.

Follow the steps below to see your submitted SNPs:

1.

Go to the dbSNP home page and locate the “Submission Information” section.

2.

Locate the link “By Submitter” in the “Submitter Information” section — it is the first selection — and click on it. You will go to the “Search/View Submitter Detail” page.

3.

Type your Handle into the empty text box on the page, make sure the radio buttons for “Submitter Handle” and “Starts With” are selected, and click the “Search” button. For this example, I will use the Handle “KWOK”.

4.

Once you press “Search” in the previous step, the “Search/View Submitter Detail” page will refresh to include a list of handles.

5.

Click on your handle (in this example, KWOK), which will take you to the SNP Submitter Contact Detail page, which will have a list of the batches you submitted.

6.

Click on the blue link for the Batch ID you are interested in to see your data. For this example I selected KWOK’s Assay link, 10.23.98, and was sent to the “View Submission Batch” page for this batch, where you can see all the data submitted in this batch.

(01/31/08)

I have a submitted SNP ID for a SNP, but the refSNP (rs) number has not yet been assigned. How do I search for this SNP without a rs number?

1.

Go to the dbSNP Home page.

2.

Go to the “Search by IDs on All Assemblies" section near the top of the page.

3.

Type the ss number you have in the text box

4.

Click on the box to the left of the text box you just filled in. This will activate a dropdown menu. Select "NCBI Assay ID (ss#)" from the dropdown menu.

5.

Click on”Search”.

The search will return a Submitted SNP Report in submission format.
(2/20/07)

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