Links from dbSNP Reports to Other Online Data Resources

The actual structure of the mutant protein does not exist. The protein containing the variations in dbSNP are mapped to neighboring proteins in the PDB database using blast analysis as described in the “Links to SNP3D Structure Mapping” section of this archive.

To view the related/neighbor structures with the variant positions labeled using an example — MAOB — go to the NCBI Related Structures Search and place your mouse on the first pink graphical sequence (1GOS-A) to see a mouse-over summary, or click it for more detail. When you get to the detail page, you can click on the “View Structure and alignment in Cn3D” button located just beneath Alignment to query sequence, to view the structure. (07/25/08)

Take a look at the 3D structure neighbor analysis appendix and the "SNP Position in 3D Structure" sub-section (in the Functional Analysis section) in the dbSNP Handbook. (5/10/07)

The SNP structure information is stored in the dbSNP FTP site SNP3D table.

1.

You can find the schema for this table by going to the dbSNP database dictionary:

2.

Select the radio buttons marked “Table Name”, and “contains”,

3.

Type the text “3D” (without the quotation marks) into the text search box.

4.

Click the Search button.

5.

The resulting screen will show you the text “SNP3D”. Click on this text to see the schema for this table. (4/30/07)

The links were computed using the co-location of the SNP and the OMIM variation positions on a gene; there is no assertion about the affect of the SNP on the disorder. (3/22/05)

The mapping of these SNPs or the gene model has changed between builds.

rs1062049 encodes a T to I amino acid change at position 21 of the MASP1 protein, which does not align with the structure at this position. MASP1 aligns with Chain A in the crystal structure of the cub1-egf-cub2 region of MASP2, starting at position 27. You can view the alignment.

dbSNP does not curate phenotypic information, but we hope to include some in the future. We do have some SNPs mapped to allelic variants in the Online Mendelian Inheritance in Man (OMIM) database.

dbSNP is an independent database and is not a division of GenBank. Sequences contained within dbSNP records are contained within the sequences of one or more GenBank records, with the GenBank records generally containing longer sequences and fewer allele designations. A diagrammatic model of the relationship between dbSNP and other NCBI databases can be found online. (04/05/06)

We have links to other NCBI databases, such as Taxonomy, Gene, OMIM, PubMed, and Structure.

1.

Go to NCBI’s LinkOut home page.

2.

Scroll down the alphabetized list of non-bibliographic LinkOut providers until you come to the following entry:
TaqMan(r) probe and primer sets from Applied Biosystems (AB)

3.

Click on the “SNP” link located to the right of the provider name to access all 4.3 million SNPs. (3/15/07)