Search variants by Chromosome and Position

Variants can be searched by providing appropriate chromosome, start and end position. These fields are mandatory. To limit search results filter criteria can optionally be modified, such as sequencing platform, variant type, allele frequency range, gene annotation and variant function. You can also subselect variants based on subgroups (e.g. Spanish). Our comparison has revealed substantial differences of SNP sets between sequencing platforms, thus we suggest to select the same platform used in your study for comparative analysis. GEEVS currently provides gene annotations based on RefSeq, Ensembl or UCSC. The search can further be restricted to specific annotation features (e.g. exotic) or variant function (e.g. non synonymous SNV). The allele frequency filter is used to obtain a subset of SNVs with limited range of allele frequencies. Supported query formats for AF are:

Search variants by Gene

Variants can be searched by providing an approved HGNC gene name or an Ensembl gene identifier. Ensembl gene identifiers only work if the Ensembl gene annotation is selected from the Gene Definition drop down menu. All other fields are optional and similar to the “Chromsome and Position” search panel explained above. Please find more info about HGNC gene names here and Ensembl gene identifers here.

Search Result Fields

Field Field Description
Chr Chromosome
Position Absolute coordinate(1-based system) on the chromosome
Reference Allele in the reference sequence
Alteration Observed allele in the sample
Allele Freq Allele frequency in the GEUVADIS exome variant server
Allele Count Alternate allele count in the GEUVADIS exome variant server
Allele Number Total allele number in the GEUVADIS exome variant server
DP Average read depth across valid samples in the GEUVADIS exome variant server
Gene The gene the variant is hit
Transcript The transcript of the gene that was hit by the variant
AAC Amino acid change in the hit transcript. Format: AA1#position#AA2, which indicates that Amino Acid 1 was changed to Amino Acid 2 at that location by the variation
Variant Function Coding region impact of the variation
Exonic Function Transcript region hit by the variant
PhyloP(Pm,Pr,vt) PhyloP conservation scores in the order of placental mammal, primates and vertebrates. You can find more about this here, at the conservation tracks.
PhastCons(Pm,Pr,vt) PhastCons conservation scores in the order of placental mammal, primates and vertebrates. You can find more about this here, at the conservation tracks.
GERP++(s1,s2) GERP++ conservation scores. You can find more about this here
SIFT Sift score for the variation
Pph2 Polyphen2 score for the variation
MutAss Mutationassessor score for the variation
Condel Condel score for the variation
Cadd1 Cadd score1
Cadd2 Cadd score2
dbSNP dbSNP rs identifier (v.138)
AF(Eur:EVS,Afr:EVS,Tot:EVS) Allele frequency in the Washington Exome variant server in ther order of European, African and Total (v.ESP5400)
AF(Eur:1000G,Afr:1000G,Amr:1000G,Asia:1000G,Tot:1000G) Allele frequency in the 1000 genomes project in the order of European, African, American, Asian and Total
SegDup Segmental Duplication score

Annotation

All the variants were annotated at the Genomic and Epigenomic Variations in Disease research group in Center for Genomic Regulation - CRG, Barcelona. Annotation was done by an inhouse developed tool with Annovar* integrated inside.

* Wang K, Li M, Hakonarson H. ANNOVAR: Functional annotation of genetic variants from next-generation sequencing data, Nucleic Acids Research, 38:e164, 2010