##################################################################################################################################################################################################################################### # Description to 95% credible set (CS95) results with VEP annotation and all meta-analysis results # # Fine name format: trait_ancestry_Credible_Sets_VEP.txt, where trait = BAS, EOS, HCT, HGB, LYM, MCH, MCHC, MCV, MON, MPV, NEU, PLT, RDW, RBC, and WBC; ancestry = AA, EA, EAS, HA, SA, and Trans. # # In each file (trait_ancestry_Credible_Sets_VEP.txt), columns 1-11 (MarkerName-PP) contain results from CS95 and trait_ancestry meta-analysis, columns 12-33 (MostSevereConsequence-gnomAD_SAS_AF) contain VEP annotation results # # (https://useast.ensembl.org/info/docs/tools/vep/vep_formats.html#other_fields), and columns 34-138 (Trans.reference_allele-Trans.gwama.effects) contain all meta-analysis results in the order of Trans (MRMEGA), EA, EAS, AA, HA,# # SA and Trans.gwama (GWAMA). (https://www.geenivaramu.ee/en/tools/mr-mega, https://www.geenivaramu.ee/en/tools/gwama-tutorial) # ##################################################################################################################################################################################################################################### MarkerName: unique marker ID (chromosome:position_allele1_allele2, with alleles listed in lexicographical order or based on indel length) Sentinel_MarkerName: unique marker ID of the setinel variant in a locus defined by +/- 250-kb region of a genome-wide significant variant (P<5E-9) - see Statistical fine mapping in Methods section Sentinel_EA: effect allele of the sentinel variant Sentinel_EAF: effect allele frequency of the sentinel variant Sentinel_P....value_association: sentinel variant's p-value from the trait_ancestry meta-analysis N.CC: number of variants selected in the CS95 EA: effect allele EAF: effect allele frequency P.value_association: p-value from the trait_ancestry meta-analysis lnBF: log Bayes Factor PP: posterior probability that the variant is causal MostSevereConsequence: most severe consequence of the variant Consequence: consequence type of the variant IMPACT: impact modifier for the consequence type SYMBOL: gene symbol Protein_position: relative position of amino acid in protein Amino_acids: only given if the variant affects the protein-coding sequence SIFT: the SIFT prediction and/or score, with both given as prediction(score) PolyPhen: the PolyPhen prediction and/or score AFR_AF: Frequency of existing variant in 1000 Genomes combined African population AMR_AF: Frequency of existing variant in 1000 Genomes combined American population EAS_AF: Frequency of existing variant in 1000 Genomes combined East Asian population EUR_AF: Frequency of existing variant in 1000 Genomes combined European population SAS_AF: Frequency of existing variant in 1000 Genomes combined South Asian population gnomAD_AF: Frequency of existing variant in gnomAD exomes combined population gnomAD_AFR_AF: Frequency of existing variant in gnomAD exomes African/American population gnomAD_AMR_AF: Frequency of existing variant in gnomAD exomes American population gnomAD_ASJ_AF: Frequency of existing variant in gnomAD exomes Ashkenazi Jewish population gnomAD_EAS_AF: Frequency of existing variant in gnomAD exomes East Asian population gnomAD_FIN_AF: Frequency of existing variant in gnomAD exomes Finnish population gnomAD_NFE_AF: Frequency of existing variant in gnomAD exomes Non-Finnish European population gnomAD_OTH_AF: Frequency of existing variant in gnomAD exomes combined other combined populations gnomAD_SAS_AF: Frequency of existing variant in gnomAD exomes South Asian population Trans.reference_allele: reference/effect allele in trans-ethnic (MRMEGA) meta-analysis Trans.other_allele: other/non effect allele in trans-ethnic (MRMEGA) meta-analysis Trans.eaf: reference/effect allele frequency in trans-ethnic (MRMEGA) meta-analysis Trans.n_samples: total number of samples in trans-ethnic (MRMEGA) meta-analysis Trans.n_studies: total number of cohorts, where the marker was present in trans-ethnic (MRMEGA) meta-analysis Trans.effects: effect direction across cohorts (+ positive effect of effect allele, '-' - negative effect of effect allele,'?' - missing data) in trans-ethnic (MRMEGA) meta-analysis Trans.beta_0: effect of intercept of meta-regression in trans-ethnic (MRMEGA) meta-analysis Trans.se_0: standard error of intercept of meta-regression in trans-ethnic (MRMEGA) meta-analysis Trans.beta_1: effect of first PC of meta-regression in trans-ethnic (MRMEGA) meta-analysis Trans.se_1: standard error of first PC of meta-regression in trans-ethnic (MRMEGA) meta-analysis Trans.beta_2: effect of 2nd PC of meta-regression in trans-ethnic (MRMEGA) meta-analysis Trans.se_2: standard error of 2nd PC of meta-regression in trans-ethnic (MRMEGA) meta-analysis Trans.beta_3: effect of 3rd PC of meta-regression in trans-ethnic (MRMEGA) meta-analysis Trans.se_3: standard error of 3rd PC of meta-regression in trans-ethnic (MRMEGA) meta-analysis Trans.beta_4: effect of 4th PC of meta-regression in trans-ethnic (MRMEGA) meta-analysis Trans.se_4: standard error of 4th PC of meta-regression in trans-ethnic (MRMEGA) meta-analysis Trans.chisq_association: chisq value of the association in trans-ethnic (MRMEGA) meta-analysis Trans.ndf_association: number of degrees of freedom (ndf) of the association in trans-ethnic (MRMEGA) meta-analysis Trans.P.value_association: p-value of the association in trans-ethnic (MRMEGA) meta-analysis Trans.chisq_ancestry_het: chisq value of the heterogeneity due to different ancestry in trans-ethnic (MRMEGA) meta-analysis Trans.ndf_ancestry_het: ndf of the heterogeneity due to different ancestry in trans-ethnic (MRMEGA) meta-analysis Trans.P.value_ancestry_het: p-value of the heterogeneity due to different ancestry in trans-ethnic (MRMEGA) meta-analysis Trans.chisq_residual_het: chisq value of the residual heterogeneity in trans-ethnic (MRMEGA) meta-analysis Trans.ndf_residual_het: ndf of the residual heterogeneity in trans-ethnic (MRMEGA) meta-analysis Trans.P.value_residual_het: p-value of the residual heterogeneity in trans-ethnic (MRMEGA) meta-analysis Trans.lnBF: log of Bayes factor in trans-ethnic (MRMEGA) meta-analysis Trans.Comments: reason why marker was not analysed in trans-ethnic (MRMEGA) meta-analysis chi.squared_association_GCcorr: genomic control (GC) corrected Trans.chisq_association p.value_association_GCcorr: GC corrected Trans.P.value_association chi.squared_ancestry_het_GCcorr: GC corrected Trans.chisq_ancestry_het p.value_ancestry_het_GCcorr: GC corrected Trans.P.value_ancestry_het EA.reference_allele: reference/effect allele in EA meta-analysis EA.other_allele: other/non effect allele in EA meta-analysis EA.eaf: reference/effect allele frequency in EA meta-analysis EA.beta: effect in EA meta-analysis EA.se: standard error of effect in EA meta-analysis EA.p.value: p-value in EA meta-analysis EA.p.value_GCcorr: GC corrected p-value in EA meta-analysis EA.q_statistic: Cochran's heterogeneity statistic in EA meta-analysis EA.q_p.value: Cochran's heterogeneity statistic's p-value in EA meta-analysis EA.i2: Heterogeneity index I2 by Higgins et al 2003 in EA meta-analysis EA.n_studies: Number of studies with marker present in EA meta-analysis EA.n_samples: Number of samples with marker present (will be NA if marker is present in any input file where N column is not present) in EA meta-analysis EA.effects: Summary of effect directions ('+' - positive effect of reference allele, '-' - negative effect of reference allele, '0' - no effect (or non-significant) effect of reference allele, '?' - missing data) in EA meta-analysis EAS.reference_allele: reference/effect allele in EAS meta-analysis EAS.other_allele: other/non effect allele in EAS meta-analysis EAS.eaf: reference/effect allele frequency in EAS meta-analysis EAS.beta: effect in EAS meta-analysis EAS.se: standard error of effect in EAS meta-analysis EAS.p.value: p-value in EAS meta-analysis EAS.p.value_GCcorr: GC corrected p-value in EAS meta-analysis EAS.q_statistic: Cochran's heterogeneity statistic in EAS meta-analysis EAS.q_p.value: Cochran's heterogeneity statistic's p-value in EAS meta-analysis EAS.i2: Heterogeneity index I2 by Higgins et al 2003 in EAS meta-analysis EAS.n_studies: Number of studies with marker present in EAS meta-analysis EAS.n_samples: Number of samples with marker present (will be NA if marker is present in any input file where N column is not present) in EAS meta-analysis EAS.effects: Summary of effect directions ('+' - positive effect of reference allele, '-' - negative effect of reference allele, '0' - no effect (or non-significant) effect of reference allele, '?' - missing data) in EAS meta-analysis AA.reference_allele: reference/effect allele in AA meta-analysis AA.other_allele: other/non effect allele in AA meta-analysis AA.eaf: reference/effect allele frequency in AA meta-analysis AA.beta: effect in AA meta-analysis AA.se: standard error of effect in AA meta-analysis AA.p.value: p-value in AA meta-analysis AA.p.value_GCcorr: GC corrected p-value in AA meta-analysis AA.q_statistic: Cochran's heterogeneity statistic in AA meta-analysis AA.q_p.value: Cochran's heterogeneity statistic's p-value in AA meta-analysis AA.i2: Heterogeneity index I2 by Higgins et al 2003 in AA meta-analysis AA.n_studies: Number of studies with marker present in AA meta-analysis AA.n_samples: Number of samples with marker present (will be NA if marker is present in any input file where N column is not present) in AA meta-analysis AA.effects: Summary of effect directions ('+' - positive effect of reference allele, '-' - negative effect of reference allele, '0' - no effect (or non-significant) effect of reference allele, '?' - missing data) in AA meta-analysis HA.reference_allele: reference/effect allele in HA meta-analysis HA.other_allele: other/non effect allele in HA meta-analysis HA.eaf: reference/effect allele frequency in HA meta-analysis HA.beta: effect in HA meta-analysis HA.se: standard error of effect in HA meta-analysis HA.p.value: p-value in HA meta-analysis HA.p.value_GCcorr: GC corrected p-value in HA meta-analysis HA.q_statistic: Cochran's heterogeneity statistic in HA meta-analysis HA.q_p.value: Cochran's heterogeneity statistic's p-value in HA meta-analysis HA.i2: Heterogeneity index I2 by Higgins et al 2003 in HA meta-analysis HA.n_studies: Number of studies with marker present in HA meta-analysis HA.n_samples: Number of samples with marker present (will be NA if marker is present in any input file where N column is not present) in HA meta-analysis HA.effects: Summary of effect directions ('+' - positive effect of reference allele, '-' - negative effect of reference allele, '0' - no effect (or non-significant) effect of reference allele, '?' - missing data) in HA meta-analysis SA.reference_allele: reference/effect allele in SA meta-analysis SA.other_allele: other/non effect allele in SA GWAS SA.eaf: reference/effect allele frequency in SA GWAS SA.beta: effect in SA GWAS SA.se: standard error of effect in SA GWAS SA.p.value: p-value in SA GWAS SA.p.value_GCcorr: GC corrected p-value in SA GWAS SA.n_samples: Number of samples with marker present in SA GWAS SA.imputation: Imputation quality in UKBB SA samples Trans.gwama.reference_allele: reference/effect allele in Trans.gwama meta-analysis Trans.gwama.other_allele: other/non effect allele in Trans.gwama meta-analysis Trans.gwama.eaf: reference/effect allele frequency in Trans.gwama meta-analysis Trans.gwama.beta: effect in Trans.gwama meta-analysis Trans.gwama.se: standard error of effect in Trans.gwama meta-analysis Trans.gwama.p.value: p-value in Trans.gwama meta-analysis Trans.gwama.p.value_GCcorr: GC corrected p-value in Trans.gwama meta-analysis Trans.gwama.q_statistic: Cochran's heterogeneity statistic in Trans.gwama meta-analysis Trans.gwama.q_p.value: Cochran's heterogeneity statistic's p-value in Trans.gwama meta-analysis Trans.gwama.i2: Heterogeneity index I2 by Higgins et al 2003 in Trans.gwama meta-analysis Trans.gwama.n_studies: Number of studies with marker present in Trans.gwama meta-analysis Trans.gwama.n_samples: Number of samples with marker present (will be NA if marker is present in any input file where N column is not present) in Trans.gwama meta-analysis Trans.gwama.effects: Summary of effect directions ('+' - positive effect of reference allele, '-' - negative effect of reference allele, '0' - no effect (or non-significant) effect of reference allele, '?' - missing data) in Trans.gwama meta-analysis