Quick start

Analysis of one SNP set

  1. In step 1, expand "Paste data" field - this SNP set (genomic coordinates) will be selected for the analyses. Alternatively, upload a file with genomic coordinates in BED format, or rsIDs of your SNPs of interest.
  2. In step 2, expand "Upload custom background"-"Paste data" fields - this "background" SNP set will be used to estimate associations that can happen by chance. If uploading a file, ensure all SNPs selected in Step 1 are included in the background SNP set.
  3. In step 3, expand "Choose regulatory datasets" field, expand "ENCODE" category and select "Histone" subcategory.
  4. Hit "Submit job" - the analysis should take a minute. The results should look like http://www.integrativegenomics.org/results_shiny?job_id=example1

Analysis of multiple SNP sets

  1. In step 1, click "diseases" button in the "Demo SNP sets" section;. This will automatically load several disease-associated SNP sets for analysis.
  2. In step 2, expand "Upload custom background"-"Paste data" fields - this "background" SNP set will be used to estimate associations that can happen by chance.
  3. In step 3, expand "Choose regulatory datasets" field, expand "ROADMAP" category and select "Histone_bPk" subcategory.
  4. Hit "Submit job" - the analysis should take a minute. The results should look like http://www.integrativegenomics.org/results_shiny?job_id=example2

To get more individual disease- or trait-specific sets of SNPs, to be uploaded in Step 1, explore https://github.com/mdozmorov/gwas2bed repository. See BED file example systemic_lupus_erythematosus.bed


To get more regulatory/epigenomic datasets, to be uploaded in Step 3, advanced features, explore https://github.com/mdozmorov/gwas2bed/tree/master/trynka-raychaudhuri repository. See BED file example H3K4me3_CD34_Cultured_Cells.bed