SNiPA – a single nucleotide polymorphisms annotator and browser

posted in: Resources

Update: 5 August 2023 – SNiPA is back, after it fell victim to a cyber attack on the Helmholtz Center Munich earlier this year.

SNiPA v3.4 (November 2020)

This is a silent update of SNiPA annotations that extends version 3.3. It comprises updated variant-phenotype associations and annotations as contained in the Ensembl 100 release, as well as new data on mQTL and pQTL associations (see release notes)
The SNiPA Variant Browser shows variants (top), genes (center) and regulatory regions (bottom)

SNiPA v3.3 (released June 2018)

Key news: Latest proteomics GWAS and most recent GWAS catalogue

pQTL data

We updated SNiPA to contain genome-wide significant pQTL association data from the pGWAS study in blood published this month by Sun et al. 2018. SNiPA version 3.3 now includes more than 16,500 cis- and trans-associations with blood protein levels.

Variant associations

For variant associations, we only updated association datasets that changed from Ensembl87 to Ensembl92. The following table shows these datasets and association counts:

SourceN (unique)ReferenceVersion
HGMD75,910 (68,320)PMID: 24077912Ensembl 92
ClinVar335,828 (308,521)PMID: 24234437Ensembl 92
OMIM variation24,028 (22,220) 92
GWAS Catalog67,764 (63,808)PMID: 19474294Ensembl 92 – r2018-05-29

SNiPA v3.2 (released March 2017)

Genome assembly: GRCh37.p13   Ensembl version: 87   1000 genomes: phase 3 version 5

SNiPA now includes more than half a million metabolite QTL associations and additionally 15,000 protein QTL associations from our 2017 proteomics GWAS. Further updates include CADD version 1.3 and updates to the most recent versions of phyloP and phastCons.

SNiPA – a single nucleotide polymorphisms annotator and browser

Need to transfer information from one SNP to another via LD? Use our web-server SNiPA –

Linking genes and functional information to genetic variants identified by association studies remains difficult. Resources containing extensive genomic annotations are available but often not fully utilized due to heterogeneous data formats. To enhance their accessibility, we integrated many annotation datasets into a user-friendly webserver.

My favorite function is the BLOCK ANNOTATION. This feature allows you to enter a single sentinel SNP identifier, and then retrieve all information that is attached to any SNP that is in LD with the sentinel SNP. This is a great way of finding out what is known about a new GWAS hit.

Another powerful function is the REGIONAL ASSOCIATION PLOT. Enter a list of SNPs with their associated GWAS p-values for a locus, and get a fully interactive and richly annotated association plot back.

Source: SNiPA – a single nucleotide polymorphisms annotator and browser (published in Bioinformatics, 31:1334-1336, 2014)