Liver chromatin accessibility QTL data (Currin et al. AJHG 2021)
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Liver chromatin accessibility QTL data (Currin et al. AJHG 2021)
| Summary statistics for chromatin accessibility quantitative trait loci (caQTL) mapped in bulk human liver tissue (n=20) using RASQUAL. One analysis used variants within 100 kilobases (kb) of ATAC-seq peak centers, and one used variants within 1 kb of peak centers. Columns: 1. peak: peak ID 2. var_ID: chromosome:position of the variant, hg19 3. chr: chromosome 4. var_position_hg19: genomic position of the variant, hg19 5. ref_allele: reference base 6. alt_allele: alternate base 7. alt_allele_frequency: frequency of the alternate allele in the 20 samples 8. HWE_Chi_square_statistic: deviation from HWE 9. imputation_quality_score: imputation score 10. log_10_Benjamini_Hochberg_Qvalue: could use for filtering 11. chi_square_statistic_(2xlogLikelihood_ratio): used for calculating p-values 12. effect_size_(Pi): dosage of the alternate allele 13. sequencing_mapping_error_rate_(Delta): used in the RASQUAL model 14. reference_allele_mapping_bias_(Phi): used in the RASQUAL model 15. overdispersion: used in the RASQUAL model 16. SNP_ID_within_the_region 17. no._of_feature_SNPs: number of SNPs within the peak 18. no._of_tested_SNPs: number of SNPs in the tested region (100kb or 1kb) 19. no._of_iterations_for_null_hypothesis: RASQUAL model diagnostic 20. no._of_iterations_for_alternative_hypothesis: RASQUAL model diagnostic 21. random_location_of_ties_(tie_lead_SNP_only_useful_with_-t_option): not relevant for this analysis 22. log_likelihood_of_the_null_hypothesis: RASQUAL model diagnostic 23. convergence_status_(0=success): RASQUAL model diagnostic 24. squared_correlation_between_prior_and_posterior_genotypes_(fSNPs): Correlation between genotypes estimated by RASQUAL from the ATAC-seq data with genotypes provided in the VCF file, using only SNPs in the peak 25. squared_correlation_between_prior_and_posterior_genotypes_(rSNP): Correlation between genotypes estimated by RASQUAL from the ATAC-seq data with genotypes provided in the VCF file, using all tested SNPs in the test window |
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| Files for download: |
| RASQUAL results, 1 kb analysis: RASQUAL-results_1kb-20samples.txt.gz size: 38 Mb |
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| RASQUAL results, 100 kb analysis: RASQUAL-results_100kb-20samples.txt.gz size: 2.2 Gb |
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| Raw p-values and eigenMT-adjusted p-values for the lead variant per peak Columns: 1. var: variant ID in the format chromosome:position_ref/alt, hg19 2. gene: peak ID 3. p-value: raw p-value for the peak lead variant calculated from the RASQUAL chi square statistic 4. BF: eigenMT-adjusted p-value 5. TESTS: number of LD-independent SNPs in the tested region |
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| Files for download: |
| eigenMT results, 1 kb analysis eigenMT-results_1kb-20samples.txt.gz size: 4.5 Mb |
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| eigenMT results, 100 kb analysis eigenMT-results_100kb-20samples.txt.gz size: 5 Mb |
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