Related Metabolic Trait Results (initial release Feb 2007)

Summary


PDF

Detailed Results for Type 2 Diabetes

  • Description of downloadable tables
    Presented for online browsing are the top SNP results with a permuted (if actually genotyped) or nominal (un-permuted) multi-marker tested SNPs with p-values less than 0.001, sorted in rank order. A full tab-delimited file containing all ~560,000 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, complete with links to help pages to plink, the analysis software package which was used to perform the analysis.

    Header Description
    CHR Chromosome Location
    PHYS_POS Physical position (according to NCBI build 35)
    SNP SNP identifier (“i_” flag denotes tested SNP by multi-marker imputation)
    EMP1 Empirical p-value after permutation within clusters (or unpermuted p-value for multi-marker SNPs)
    NP Number of permutations for this SNP p-value is based on
    CHISQ_CMH Raw Cochran-Mantel-Haenszel test statistic
    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
    CHISQ Raw Armitage Trend Test (Chi-squared)
    A1 Minor allele
    A2 Major allele
    MAF Frequency of A1 allele (entire 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 Whole sample HW p-value
    P_HWD_A Cases-only HW p-value
    P_HWD_U Controls-only HW p-value
    F_MISS Overall frequency of missing data for this SNP
    F_MISS_A Frequency of missing data in affected
    F_MISS_U Frequency of missing data in unaffecteds
    P_MISS p-value for affected/unaffected differential missing data test
    RANK Rank order of the SNP over all tested SNPs (according to EMP1)
    Note: Headers apply to all results files for the DGI 500K Whole Genome Data.

  • Instructions for using the results files
  • Related Metabolic Traits Detailed Results Table:      
       
    Trait Type Trait Name Description of Trait (PDF) Table of Top Single
    Marker Results for Association (HMTL)    		 Table of All Single
    Marker Results for Association (txt)
    Glucose Trait        
      Fasting glucose pending * *
      HOMA-IR * * *
      Insulinogenic index * * *
    Obesity Traits        
      Body mass index *  
      Cases * *
      Controls * *
      Weight *  
      Cases * *
      Controls * *
      Height * *  
      Cases * *
      Controls * *
      Waist circumference *  
      Cases * *
      Controls * *
      Waist hip ratio *  
      Cases * *
      Controls * *
    Lipid Traits        
      ApoA1 * * *
      ApoA2 * * *
      ApoB * * *
      LDL cholesterol * * *
      HDL cholesterol * * *
      Triglycerides * * *
      Triglyceride/HDL cholesterol ratio * * *
    Blood Pressure Traits        
      Diastolic blood pressure pending * *
      Systolic blood pressure pending * *
      Hypertension pending * *