SNPsnap
Match your SNPs with SNPsnap!
A fast and easy entry point to match and annotate 1000 Genome SNPs.
What's New?
July 30, 2015
No matching of X chromosome SNPs
SNPsnap is not able to match X chromosome SNPs. Input X chromosome SNPs are still accepted but they will be excluded during the matching algorithm (exclusion mark:
SNP_genetic_properties_corrupted_in_data_base).
We are sorry about the inconvenience this may cause our users.
March 18, 2015
Download SNPsnap's Annotation Files
SNPsnap now offers to download SNPsnap's annotation database.
Check it out here
March 10, 2015
Major SNPsnap update: 1000G Phase 3 Data
SNPsnap have undergone a major update. Here is the list of new features:
- SNPsnap is now based on 1000 Genome Phase 3 data. The old Phase 1 data is no longer supported.
- Super populations (European, EUR; East Asian, EAS; West African, WAFR) are added to allow more specific SNP matching based on your study population.
- X-chromosome SNPs included.
- Geneset updated to GENCODE genes.
- New SNPsnap annotation features: MAF, HGNC symbols, distance to nearest protein coding gene, flag for SNP within gene and more.
- SNPsnap now uses the lightning fast PLINK 1.9 for clumping input SNPs.
September 15, 2014
Let SNPsnap check the independence of your input SNPs
Checking indepence of SNPs have never been easier: we have integrated an option for reporting the independence of your input SNPs. You can adjust the threshold of clumping (both LD and physical distance) after selecting the checkbox Report input loci independence. This will generate the file input_snps_clumped.txt where researches can inspect the clumping in more details.
September 11, 2014
Accepting rs-numbers
SNPsnap now accepts rs-numbers as SNP input. In addition SNPsnap generates the file input_snps_identifer_mapping.txt to ease the mapping to/from chromosomal coordinates and rs-numbers.
July 14, 2014
Maching Bias
SNPsnap now includes a matching bias calculation to determine differences between the mean genetic properties of input and matched SNPs.
This helps the user to balance the trade-off between requesting a large number of matched SNPs while avoiding systematic differences between input and matched SNPs.
This helps the user to balance the trade-off between requesting a large number of matched SNPs while avoiding systematic differences between input and matched SNPs.
July 8, 2014
Option for excluding HLA SNPs
SNPsnap now supports a new exclusion feature Exclude HLA SNPs.
Enabling this option will exclude all input SNPs mapping to the HLA region (chr 6 25Mb-35Mb) in both input and matched SNPs.
Enabling this option will exclude all input SNPs mapping to the HLA region (chr 6 25Mb-35Mb) in both input and matched SNPs.
June 25, 2014
SNPsnap is now airborn!
The team behind SNPsnap is excited to announce that SNPsnap is now online.
We strongly encourage you to provide feedback for any improvements to the website or SNP matching parameters.
We strongly encourage you to provide feedback for any improvements to the website or SNP matching parameters.
© Broad 2014
