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Genomatix GeneGrid

Genomic variants like single nucleotide polymorphisms (SNPs) or small insertions / deletions (InDels) are of major interest to biologists and clinicians alike. Their impact ranges from determining your eye color to influencing response to medication. They can cause cardiovascular or neurodegenerative diseases, induce cancer or trigger resistance to HIV infection. Identifying causal variants is crucial for the understanding of molecular mechanisms and diagnostics of rare or common diseases. With today’s Next Generation Sequencing (NGS) technologies it is possible to detect millions of variants within an individual genome through a single experiment. One question remains, though:
Which are the relevant ones?

Genomatix GeneGrid technology enables you to quickly reduce millions of variants to the few or even the single relevant one(s).

All known & novel SNPs in your results can be annotated using our extensive annotation.You can immediately find those variants of interest to you, perform trio analyses, compare case and control sets (using multiple samples) or identify somatic SNPs within minutes.

Viewing the genomic location of a SNP in our Genome Browser directly from GeneGrid and the interaction with the Genomatix Pathway System to explore networks of affected genes allows for an in-depth assessment of the biological background of your variants.

Finally the extensive reports generated by GeneGrid provide you with all the known biological and biomedical information for your list of SNPs at a glance.

You can access GeneGrid at its dedicated page at

Gene Grid Annotation / Filters

This annotation can be used in GeneGrid to find variants of relevance

Genomic location
  • Chr
  • Band
  • Position (bp)
Variant description
  • Alt2 allele
  • Other alternative alleles
Feature annotation
  • Known variant
  • Known gene
  • Gene name
  • Exome
Predicted molecular effects on protein
  • Low confidence
  • Consensus variation
Variant quality
  • Genotype quality
  • Applied filters
Population allele frequencies
  • gAF
  • espMAF
  • ExAC
Regulatory annotation
  • Regulatory feature
Experimental evidence
  • Transcription factor binding
  • Matched binding motif
  • DNaseI hypersensitivity
  • Histone modification
Gene ontology
  • GO processes
  • GO functions
  • GO components
Computational protein effect predictions
  • SIFT
  • SIFT pred
Evolutionary conservation
  • GERP
  • SiPhy-Pi
  • SiPhy-Omega
Literature mining
  • Citations
  • Literature diseases
  • Literature tissues
Clinical and diagnostic annotation
  • Diagnostic tests
  • Diagnostic diseases
  • Clinical significance
  • Clinical diseases
  • Somatic mutation frequency
  • Somatic mutation tissues
  • Popular gene panels
Comparison summary

- general:
  • Difference between groups
  • Difference in case group
- for trios:
  • Compound heterozygosity
  • Offspring inheritance
- for cancer:
  • Difference pairwise somatic
  • Somatic