Whole Genome Scan for Type 2 Diabetes in a Scandinavian Cohort

Type 2 Diabetes Results (updated March 2007)

in

Results Summary


PDF

Detailed Results for Type 2 Diabetes

  • Description of downloadable tables
    Presented for online browsing are the top SNP results (if actually genotyped) and nominal multi-marker tested SNPs with p-values less than 0.001, ranked by p-value. A full tab-delimited file containing all 671,699 tests performed is available for download. Multi-marker tests were performed using the two best-SNP proxies based on the CEU HapMap project data (see Pe’er et al. 2006 for details), and a list of these informative proxy SNPs used for the test are available for download. The material available for online browsing contains the following information:

    Note: Headers apply to all results files for the DGI 500K Whole Genome Data.

  • CHR Chromosome Location
    PHYS_POS Physical position (according to NCBI build 35)
    SNP SNP identifier (“i_” flag denotes tested SNP by multi-marker imputation)
    Z_PVAL P-value of the Z-score test statistic
    ZSCORE Z-score statistic for Population/Familial sample meta-analysis
    OR_CMH Odds Ratio for CMH test
    L95 Lower 95% CI for odds ratio for CMH odds ratio
    U95 Upper 95% CI for odds ratio for CMH odds ratio
    A1 Minor allele in Population-based case/control sample
    A2 Major allele in Population-based case/control sample
    MAF Frequency of A1 allele in Population-based case/control sample
    F_A Frequency of A1 in all affecteds
    F_U Frequency of A1 in all unaffecteds
    GENO Genotype counts in whole sample (A1 homozygous/heterozygous/A2 homozygous)
    GENO_A Genotype counts in affecteds
    GENO_U Genotype counts in unaffecteds
    P_HWD P-value for Hardy-Weinberg test (all samples)
    P_HWD_A P-value for Hardy-Weinberg test (cases only)
    P_HWD_U P-value for Hardy-Weinberg test (controls samples)
    F_MISS Overall frequency of missing data for this SNP
    F_MISS_A Frequency of missing data in affecteds
    F_MISS_U Frequency of missing data in unaffecteds
    P_MISS P-value for affected/unaffected differential missing data test
    GENE_LIST Annotation of genes within 30kb of the SNP
    RANK Rank order of the SNP over all tested SNPs (according to GC)

    Note: Headers apply to all results files for the DGI 500K Whole Genome Data.

  • Table of the Top Single Marker and Multi-Marker Results for Association to Type 2 Diabetes in 2931 Scandinavian Patients (html) updated March 2007
  • Table of all Single Marker and Multi-Marker Results for Association to Type 2 Diabetes in 2931 Scandinavian Patients (text) updated March 2007
  • Instructions for using the results files