How do I use Affymetrix IDs to find dbSNP refSNP (rs) numbers? The Affymetrix ID is: SNP_A-1508104

There are two methods you can use to search for the refSNP number using the Affymetrix ID:

Method #1:

1.

Go to the dbSNP home page and select Entrez SNP from the dbSNP search options located just above the announcement section.

2.

When you get to the Entrez SNP page, click on the Preview/Index tab located at the top of the page just below the search box.

3.

Once on the Preview/Index page, click on the arrow next to the text box that reads “All Fields” to release a drop down menu.

4.

Scroll down the drop-down menu and select “Submitter SNP ID”

5.

In "Preview/Index" tab, choose "Submitter SNP ID" in drop down field, and place your Affymetrix ID in the empty text box to the right, and click the “preview” button.

Method #2:

1.

Go back to the dbSNP home page, and go to the “Search by IDs on All Assemblies” section, and Click the arrow next to the text box that says ”Reference Cluster ID(rs#)”. This will open a drop-down menu.

2.

Select “Submitter SNP ID” (your Affymetrix ID is the SNP ID the Submitter gave to it, thus “Submitter SNP ID”).

3.

Place your Affymetrix ID in the text box to the left of the one that now reads “Submitter SNP ID”, and press the “Search” button.

Your specific Affymetrix SNP ID did not turn up a match, so try the following:

1.

Go back to the “Search by IDs on All Assemblies” section in the dbSNP home page, and click the arrow next to the text box that says ”Reference Cluster ID(rs#)” to re-open the drop-down menu.

2.

Select “Submitter SNP ID”

3.

Place the following truncated search term in the text box to the left: SNP_A-15*

4.

Press the search button.

The result page for this search does at least indicate that dbSNP does contain SNPs with similar ID numbers (i.e. SNP_A-1507972http://www.ncbi.nlm.nih.gov/SNP/snp_viewTable.cgi?handle=AFFY). (7/27/07)

I inquired about Affymetrix number "SNP_A-1508104", and just heard back from Affymetrix. Apparently, SNP_A-1508104 is on their "10K 2.0 array", for which dbSNP does not yet have information — this would explain why we could not find this Affymetrix number in dbSNP.

Affymetrix tech support confirmed that SNP_A-1508104 does indeed correspond to rs1374108. (I think Affymetrix downloads dbSNP data and then uses the information in making their chips. That is why they know the corresponding refSNP[rs] number). Affymetrix recently submitted the sequences from four of their chip products to dbSNP (see below):

Mapping250K_Nsp

Mapping250K_Sty

Mapping50K_Hind240

Mapping50K_Xba240.

To access dbSNP data for the SNPs on these chips, users can query dbSNP by using the Affymetrix ID number. You can find more information at the Affymetrix site. (8/03/07)

I followed the instructions in the FAQs and can find rs IDs for Celera IDs starting with hCV, but not for Celera IDs starting with hDV.

Celera did not submit all of their variations to dbSNP. We have most (but not all) of Celera’s human (hCV*) and mouse (mCV*) variations, but we don't have any that starts with hDV*.(02/22/08)

How do I use Celera ID numbers to find dbSNP refSNP (rs) numbers?

1.

Go to the SNP home page

2.

In the “Search by IDs” section of the home page, type the Celera ID number in the text box, and select “Celera SNP ID” from the drop down menu to the right of the text box.

3.

Click on the “Search” button.(3/3/06)

How do I search for rs numbers that correspond to a list of hCV (Celera) SNP numbers? When I tried to “Search by ID", I got an ss number but not an rs number.

The reason why your list of hCV numbers has associated submitted SNP (ss) numbers but not refSNP (rs) numbers is that these particular variations have not yet been mapped and clustered.

rs numbers have not been assigned for these ss numbers in the current build. They will be automatically assigned during the next dbSNP build mapping and clustering process, and will be available when the new build is released. Information about the dbSNP rs numbering and clustering process is available in the dbSNP handbook.

To receive notification of new build releases, subscribe to dbSNP-announce. (2/16/06).

When I run a Batch query using Celera/ABI SNP IDs, the Chromosome report I get back doesn't contain the original query IDs, and is sorted by rs number, so I've lost correlation between the IDs. What can I do?

Only the FLATFILE report lists the submitter's ID (i.e. in your case, the hCV IDs) of all submitted SNPs. hCV IDs, however, are not reported for SNPs that are submitted by an entity other than Celera.

dbSNP does not have control over the assignment of specific rs numbers to hCV IDs. Not every rs number has a corresponding hCV ID, and Celera may change or drop the rs number based on their internal processing. Likewise, dbSNP’s mapping and clustering process may change, merge, or drop rs numbers. I suggest that you convert your processing from hCV to dbSNP rs numbers, since rs numbers are the standard identifier for SNP.

There is a table of hCV IDs and their corresponding rs and ss numbers (for dbSNP build 127) located in in dbSNP’s FTP site in the misc. folder of the human_9606 directory. The file name is hCV_dbSNP_ID.txt.gz. The column definitions are located in the hCV_dbSNP_ID readme file located in the same directory and folder. (2/13/07)

Where can I search for variations using HGVS nomenclature?

There are two places you can use to search for variations using HGVS nomenclature:

Go to the “Search by IDs on All Assemblies” section of the dbSNP home page, and select “HGVS names” from the dropdown menu.

OR

Use the Human Variation: Search, Annotate, Submit site

(04/17/08)

I am trying to find an rs number for a SNP called CD14-159C/T. Can you tell me what the rs number is or how I can find it?

You can use the Human Variation: Search, Annotate, Submit site to find the rs number you need, but you’ll need the accession number for the reference sequence that codes for CD14 to do so. (04/09/08)

Will the HGVS based variation search you are testing also be available through eutils?

Yes, it should also be available through eutils once we have finished developing the resource (9/27/07)

Can you tell me how to find the rs number for a SNP when we have just position [TNFa (-308G/A) ] to search with?

Use the Human Variation: Search, Annotate, Submit site,which performs a position search using names based on HGVS recommended nomenclature (e.g. NM_000594.2:c.-308G>A) that you can try, but in order to do so, you’ll need to have a accession for the reference sequence (a mRNA, or protein, or a genomic sequence in GenBank). (09/07: 07/31/08)

How I match SNP names from the Seattle SNPs database (e.g. a Seattle SNPs named UI1498 in the IL10 gene) to dbSNP rs numbers in dbSNP?

Seattle SNPs names were submitted to dbSNP using the gene name concatenated with the position of the variation. For example, a couple of SNPs submitted for gene CPSF4 were submitted by Seattle SNPs as CPSF4-000171 and CPSF4-000205.

1.

To find the Seattle SNPs names you need to use to search for dbSNP IDs, go to the Seattle SNPs page for the gene of interest (our example, CPSF4). Once you’re on this page, scroll down to the “Gene Specific Links” section of the page, and select the “SNP Context” link to see a list of names used by Seattle SNPs for SNPs in this gene (please note: As we have no control over Seattle SNPs web page, the link mentioned above may change in the future from this description).

2.

Go to the “Search by IDs” section of the dbSNP homepage .

3.

Enter the Seattle SNPs names (ie.CPSF4-000171) into the text box.

4.

Click on the box located immediately to the right of the text box to activate a drop-down menu. Select “Submitter SNP ID” from the menu.

5.

Click on the “Search” box to get the corresponding refSNP (rs) number for that submitter ID. (3/7/07)

What do I enter in the "Between Markers STS Search" field in the dbSNP search window?

Enter the name or ID numbers of an STS (i.e. SHGC-156091 and D1S3135) in dbSTS. (1/7/05)

How do I find the refSNP (rs) numbers for Y chromosome markers published by the Y-chromosome consortium (e.g. what is the corresponding rs number for STS DYS190)?

1.

Enter "DYS190" into Entrez cross-database search, and click the “Go” button.

2.

You will find that there is a single hit (AF337053), which is located in the NCBI Nucleotide database. Click on the Nucleotide Icon to go to the Nucleotide result page.

3.

Click on the AF337053 link to get to the Sequence View page for this accession number. You will find the relationship between DYS190 and the human Y chromosome in the “features” section of this page:
/organism="Homo sapiens"
/mol_type="genomic DNA"
/db_xref="taxon: 9606"
/chromosome="Y"
/clone="3-11; DYS190"

4.

Click on the word“Links” at the top right corner of the sequence view page; clicking on it will release a dropdown menu. Select “Mapviewer” to see that AF337053 is located on the q11 region of Y.

5.

Click on the Y chromosome link to go to Mapviewer. Click on the “Maps & Options” button to add the "Variation" option to your Mapviewer display. Two SNPs are within 2000 bp of AF337053.(2/14/06)

Every time I search for STS markers in dbSNP, dbSNP returns a screen that says that no SNPs were found in my region of interest. What am I doing wrong?

I tested the STS search and it works for the query: between STS “RH98513” and “SHGC-74072”. For your query to work, the STS markers you use must exist in dbSTS and must be on the same chromosome. Check your markers against dbSTS to make sure that they are valid.

If I know the PubMed number of a SNP, how do I get the rs ID of this SNP?

Query Pubmed using the ID (pmid). Once you get the result, you can either select SNP Link from Display, or you can or click on the blue word Links at the top right side of the result and select SNP, if it is shown. The SNP option is not shown if there is no SNP associated with the publication.

Here’s an example of a publication with a SNP association.

How do I search for a SNP that is associated with a CGAP identifier?

dbSNP does not contain CGAP identifiers for one of two reasons: either SNPs with CGAP identifiers have not been submitted to dbSNP, or the SNPs were submitted using a different identifier.

If you know the identifier that a particular submitter has used in their submission to SNP, you can search for SNPs of interest using this identifier:

1.

Go to the dbSNP homepage

2.

Go to the Search by IDs section, and enter the SNP indentifier in the text box.

3.

Select "Submitter SNP ID” from the drop-down menu to the right of the text box and click on the "search" button located below the text box.

If you have the sequence, you could also try a BLAST search. (3/14/06)

Why does the "[ACC]" term used in SNP searches return the following error message: “The following term was not found: AC019340[ACC]”.

We only index sequence accession numbers (NT and NM) that have SNPs mapped directly to them, and do not project them onto BAC clone sequences (ie. AC000120). (3/6/07)

Finding an RS Number Using an SS Number and Vice Versa

Finding Submitter (Local) ID used for a Particular SNP

Finding Submitter Information

Finding Lists of Chromosome Positions

Finding Primers and Assay Conditions

Searching for Missing or Replaced refSNPs

I’ve tried without success to find human SNPs from a publication in dbSNP using the IDs mentioned in the article as well as the author’s name. Is there anything else I can try?

Yes, you can now submit previously published human variations described in a publication not authored by you to a new resource called Human Variation: Annotate and Submit Batch Data. You must, however, be able to describe the variations using HGVS nomenclature. You will see that the submission template for this resource has a field for the inclusion of the PubMed ID number, so that the original reference for the variation will be linked to the submission. You can also submit a single variation from the literature using the Human Variation: Search, Annotate, Submit site. Please Note: these online submission resources accept human data submissions only. (06/11/08)

I have a SNP that has no rs number, but does have a ID (human TNF alpha -308G>T), I’ve searched in dbSNP, but can’t find an rs number for it.

Unless the submitter used the exact name "human TNF alpha -308G>T "in their submission, it won't show up as a result in your dbSNP search. It is also possible that the authors who mentioned "human TNF alpha -308G>T" in their publication never submitted this SNP to dbSNP.

Submission to dbSNP is voluntary, but we do try to encourage people to submit SNPs to dbSNP prior to publication so that they can cite their assigned dbSNP IDs (ss or rs) in their manuscript. Check the publication to see if the authors included a dbSNP ID for "human TNF alpha -308G>T" in the manuscript; if they have not, try BLASTing the DNA sequence of human TNF alpha -308G>T (if you have it) against dbSNP to see if there are any matching rs numbers. If there are no matches, and you wish to see this variation in dbSNP, you can submit it yourself using the Human Variation: Annotate and Submit Batch Data page (multiple submissions) of the Human Variation: Search, Annotate, Submit site (single submission). The Human Variation: Annotate and Submit Batch Data Quick Start explains how it is possible to submit published SNPs not already housed in dbSNP. (04/30/08)

CELL. 2004; 119: 591-602 reported a MDM2 SNP309 (A/G polymorphism located in intron 1 of MDM2 gene, but I cannot find it in dbSNP.

If this is the reference you mentioned, I do not see a dbSNP accession listed. dbSNP has 358 SNPs located in the MDM2 gene region, but I do not see the specific A/G SNP in intron 1 you mentioned.

Although dbSNP currently has 17million+ human SNPs (including 7,529,694 SNPs located in genes), it is still possible that this particular SNP in the MDM2 gene was never submitted to dbSNP. dbSNP is populated by data submitted by users like yourself, and usually, they submit SNP data prior to the release of their publications. If you wish to see this variation in dbSNP, you can submit it yourself using the Variation Batch Submission page. The Variation Batch Submission Quick Start explains how it is possible to submit published SNPs not already housed in dbSNP(04/24/08)

I am trying to find an rs number for a SNP called CD14-159C/T. Can you tell me what the rs number is or how I can find it?

You can use the Human Variation: Search, Annotate, Submit site to find the rs number you need, but you’ll need the accession number for the reference sequence that codes for CD14 to do so. (04/09/08)

How do I find a refSNP (rs) number for a SNP using a reference number found in the literature?

The dbSNP GeneView (SNP linked to Gene) page may be the best way to look for a refSNP (rs) number rs that corresponds to published gene position variations. You can reach the GeneView page by clicking on the pink “GeneView” button located under the refSNP (rs) number of interest in the results page of a Entrez SNP search. Using the GeneView page may not always work if the published gene model is different that the model used in dbSNP, but in your case there is strong evidence that the SNP in position 45 is rs2241766, which is shown on the GeneView page as amino acid 15, codon position 3 (3*15) = 45. rs2441766 is located at contig position 93066042.

Looking for the other two variations is a little more difficult. First, click on the radio button labeled "in gene region", which is located in the long, grey, rectangular box found above the gene model (contig mRNA transcript) section of the GeneView page. Now click on the “refresh” button located at the far right end of the grey box where you found the in gene region" button. You will now see all SNPs near ADIPOQ (the default is cSNPs). The SNP in position 713 is likely rs3774261. I determined this by subtracting 45 from 713 (the difference in the position of the two variations) and then adding this number to the contig position of the SNP at position 45. (713-45)+ 9306642 = 93066709. rs3774261 is located at contig position 93066709. (6/1/06)

Locating SNPs using IDs Published in OMIM Articles