SNPsnap

Input

Paste in SNPs or upload a file

Load example SNPs

Paste in SNPs

File input

Upload file

See documentation - User input for detailed description of input formats.

Population

Choose population genotype data

Population*

See 1000 Genomes Project website for additional information about the population genotype data.

Locus Definition

Select your locus definition

Distance type

LD Physical Distance

Distance cut-off

r²

SNP Matching Criteria

Maximum allowable deviations for matching SNPs

Minor Allele Frequency

± % point

Gene Density

± %

Distance to Nearest Gene

± %

LD buddies

± %

using

r²

We recommend initially using the default SNP Matching Criteria. You can play with the details later!

Output Options

Requested SNPs

Number of matched SNPs

Annotation

Annotate matched SNPs*

Annotate input SNPs*

Input loci independence

Report input loci independence (clumping)

*See documentation - SNP Annotations for what genetic attributes SNPsnap currently uses for SNP annotation

SNP Exclusions

Exclude input SNPs in matched SNPs

Exclude HLA SNPs

Session Information

Please fill in information to identify your job.

Job name

Check that your SNP coordinates are from the human genome build GRCh37/hg19?
Check that your input file is valid so SNPsnap read all of SNPs?