SNPsnap


Any Questions?

We encourage that you direct any questions or feedback to the feedback formula or send the SNPsnap team an email. Thank you for helping improving SNPsnap

Browser Compatibility

Does SNPsnap support all browsers?
SNPsnap is fully compatible with Safari 7, Firefox 30 and Chrome 35. For the best user experience we encourage using Chrome 35 or newer.
Internet Explorer 11 is supported but may not provide the best user experience. Users using older versions of Internet Explorer (10 or older) may experience problems.

Variant Identifiers and Annotation

Will I be able to use rs-numbers as input SNP identifiers?
Yes. SNPsnap accepts rs-numbers and chromosomal coordinates (from GRCh37/hg19) as SNP identifiers. Please note that not all variants in the 1000 Genomes Project have been assigned a rs-number. When no rs-number is given in the 1000 Genomes data, SNPsnap uses the chromosomal coordinate as a substitute for the rs-number.
What types of variants are included in the SNPsnap database?
All types of variants listed by 1000 Genomes Project are included: single nucleotide variants (SNPs), indels and larger structural variants. Note that SNPsnap's chromosomal coordinates identifers do not describe the type of variant, as it is the case for IMPUTE-format (e.g. chr1:100123071:D or chr1:100134769:I for insertions and deletions, respectively).

Output

What gene annotations does SNPsnap use for column locus genes likeID_genes_in_matched_locus?
SNPsnap uses ~60,000 genes from the GENCODE gene set and including protein coding genes, non-coding genes and pseudo genes.
Why is there a replicated input SNPs in matched_snps.tab even though I enabled Exclude input SNPs in matched SNPs?
In the unlikely event that no matching SNPs are found, SNPsnap will fill in the input SNP instead of the matched SNPs.

Results

What are the run times for SNPsnap?
SNPsnap matching takes ~5 seconds per input SNP when requesting 10,000 SNPs (matching 100 input SNPs will take ~8 minutes to match). Run time for matching may be reduced by a factor two if less matched SNPs is requested. If any annotation option (Annotate matched SNPs or Annotate input SNPs) is enabled SNPsnap uses an additional ~2 minutes in total. If the option Report independent loci is enabled SNPsnap uses ~5 minutes for clumping 10 SNPs using default clumping thresholds (r=0.5 and kb=250). We note that the runtime for clumping is very sensitive to the clumping thresholds.
For how long are my files saved on the web server?
The SNPsnap web server stores the result files for 24 hours. After this your result files will be permanently deleted.