% GEFOS.seq/UK10K BMD Single Variant Meta-analysis % October 21, 2015 This archive contains 3 files: fa2stu.MAF0.005.pos.out fn2stu.MAF0.005.pos.out ls2stu.MAF0.005.pos.out Each file provides genome-wide meta-analysis summary statistics from GWAMA for forearm (fa), femoral neck (fn) and lumbar spine (ls) BMD, respectively. In addition to GWAS quality filtering, such as imputation quality and Hardy-Weinberg equilibrium, variants were retained if present in more than 1 study and with MAF>=0.005. For further information regarding this study, please refer to the following publication: **Zheng HF, et al. Whole-genome sequencing identifies EN1 as a determinant of bone density and fracture. Nature 2015.** ## GWAMA Output Format 1. chromosome - Marker chromosome 2. position - Marker position (bp) 3. rs_number - Marker ID 4. reference_allele - Effect allele 5. other_allele - Non effect allele 6. eaf - effect allele frequency as reported from the UK10K + 1000 Genomes reference panel. 7. beta - Overall beta value for meta-analysis 8. se - standard error of beta. 9. beta_95L - Lower 95% CI for BETA 10. beta_95U - Upper 95% CI for BETA 11. z - Z-score 12. p-value - Meta-analysis p-value 13. -log10_p-value - Absolute value of logarithm of meta-analysis p-value to the base of 10. 14. q_statistic - Cochran's heterogeneity statistic 15. q_p-value - Cochran's heterogeneity statistic's p-value 16. i2 - Heterogeneity index I2 by Higgins et al 2003 17. n_studies - Number of studies with marker present 18. 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) 19. 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) chromosome position rs_number reference_allele other_allele eaf beta se beta_95L beta_95U z p-value _-log10_p-value q_statistic q_p-value i2 n_studies n _samples effects For further information on GWAMA, visit [http://www.well.ox.ac.uk/gwama/](http://www.well.ox.ac.uk/gwama/). ## References Magi R, Morris AP: GWAMA: software for genome-wide association meta-analysis. BMC Bioinformatics 2010, 11:288