Table 1.
Some web tools dealing with SNP biological properties and their characteristics related to the prioritization of GWAS results
| Web tool | Exclusively for non-synonymous SNPs | Accepts multiple SNPs | Accepts P-values | Performs customizable GWAS prioritization | Incorporates LD proxies | Some external data sources used (Table 2) |
|---|---|---|---|---|---|---|
| F-SNP (44) | No | No | No | No | No | 1,4,5,6,9–20 |
| FastSNP (45) | No | Yes | No | No | No | 2,4,5,7,8,13,14,19 |
| GenePipe (43) | No | Yes | Yes | Yes | Yes | 2,8,13,14,17,20 |
| Panthera (46) | Yes | Noa | No | No | No | 4 |
| PolyPhen2 (9–10) | Yes | Yes | No | No | No | 2 |
| SIFT (39) | Yes | Yes | No | No | No | 2 |
| SNPs3Db (47) | Yes | Noc | No | No | No | 2 |
| SPOT (4) | No | Yes | Yes | Yes | Yes | 2,3,8,13 |
The values in the column ‘External data sources used’ refer to the ‘Number’ column in Table 2; this list of external data sources used may not be complete.
aThis is the cSNP web tool on the Panther site. The site states that a tool can be downloaded for analyzing multiple SNPs.
bWe studied the tool labeled ‘Impact on Protein Structure and Function’ on the SNPs3D main page.
cSNPs3D does offer an ‘annotate SNPs’ feature that apparently requires registration and we did not explore this.