% 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