CandiSNPer is a webtool which helps in characterizing Single Nucleotide Polymorphisms (SNPs) that are located in the vicinity of an SNP of interest (start SNP). Along with the computation of the maximal Linkage Disequilibrium (LD) region around the start SNP. CandiSNPer provides additional information with respect to the molecular consequences of the SNPs and the genes located in the LD region.

  • INPUT

    1. SNP ID

      Enter the ID of the SNP of interest (e.g. a significant SNP from a GWAS) that you want to compare with other SNPs.

    2. Population

      Choose the population (e.g. Central European).

    3. Region around SNP of interest

      Choose the initial-region for which LD should be calculated. Default is 300 kb around start-SNP.

    4. LD

      Decide which measure should be used to define LD (Linkage Disequilibrium) region. (You can chose between D' and r².)

    5. Threshold

      The program is looking for the most distant SNPs whose LD is above the chosen threshold. These two SNPs define the LD region. Default is 0.2

    6. Plot format

      Choose the format of the plot file. (PDF is always additionally generated.)

    7. Color of SNPs

      You can assign a colour to each SNP class. If an SNP belongs to several classes it is assigned the color of the highest class to which it belongs

    8. Show genes

      If you check the box the genes are shown as brown arrows in the plot.

  • OUTPUT

    Imagefile

    • The red cross is the start-SNP you have chosen (1).
    • The data points in the plot represent the LD values of SNPs (4). The color represents the functional class as specified in the input.
    • The ticks represent the SNPs with unknown LD (2). The color represents the functional class as specified in the input.
    • The two red lines define the LD region (3).
    • The horizontal green line shows the average LD plus three standard deviations for scrambled genotypes (6).
    • The horizontal brown arrows represent the genes (5).

    Textfile

    The textfile lists annotation about all SNPs in the LD region with the following columns:
    • ID of the SNP
    • Chromosome
    • Chromosomal position
    • D' (only available for HapMap-SNPs)
    • r² (only available for HapMap-SNPs)
    • Functional class
    • Nearest gene
    • Distance to nearest gene
    • Conservation score (not for all SNPs)

  • FUNCTIONAL CLASS

    A short description of the different functional classes of SNPs used by CandiSNPer:

    Name of functional classDescription
    Stop Lostcauses a loss of a stop codon
    Stop Gainedcauses a gain of a stop codon
    Frameshift CodingAn insertion or a deletion in the coding region which causes a frameshift
    Non-Synonymous CodingA change of a nucleic acid in the coding region, which causes a change of the amino acid
    Synonymous CodingA change of a nucleic acid in the coding region, which doeas not causes a change of the amino acid
    Intronicchange in intron
    Splice Sitechange 1-3 bps into an exon or 3-8 bps into an intron
    Essential Splice Sitein the first 2 or the last 2 base pairs of an intron
    5'UTRchange in transcript, upstream of the coding region
    3'UTRchange in transcript, downstream of the coding region
    UpstreamWithin 5000 bps upstream of the gene, [with respect to the strand of the gene]
    DownstreamWithin 5000 bps downstream of the gene [with respect to the strand of the gene]
    Intergenicchange outside a gene and the distance to the next gene is greater than 5000 bps
    Within non-coding genechange in a non-coding gene


  • Citation

    Schmitt, AO, Assmus J, Bortfeldt, RH, and Brockmann, GA
    CandiSNPer: a web tool for the identification of candidate SNPs for causal variants.
    Bioinformatics 26 (7) 2009. PubMed