GIANT Adult Height GWAS Summary Data and Estimated LD
The single-SNP summary statistics and estimated LD matrices for adult human height (Wood et al, 2014).
Contact
Jane Doe
Location
PPS server:
/mnt/gluster/data/internal_supp/giant_height_2014
Source
The processed data are derived from the following datasets.
- GWAS summary statitics:
https://www.broadinstitute.org/collaboration/giant/index.php
- 1000 Genomes EUR haplotypes (phase 1):
http://csg.sph.umich.edu//abecasis/MaCH/download/1000G.2012-03-14.html
- HapMap CEU genetic maps (rel#24):
https://mathgen.stats.ox.ac.uk/wtccc-software/recombination_rates/genetic_map_b36_CEU.tgz
File Summary
The GWAS summary data file height2014_analyzed_autosome_chr_*.txt
has the following columns.
MarkerName
: The dbSNP NameAllele1
: The 1st Allele (hg19 + strand)Allele2
: The 2nd Allele (hg19 + strand)Freq.Allele1.HapMapCEU
: The Allele Frequency ofAllele1
in the HapMap CEU Populationb
: Estimated Single-SNP Effect SizeSE
: Standard Errorp
: Single-SNP P-valueN
: Sample Sizepos
: Physical Position (hg19)chr
: Chromosome ID
The folder estimated_ld
contains the estimated LD (i.e. correlation) matrices, using the shrinkage estimator from Wen and Stephens (2010).
R.chr*.mat
: the hard threshold for small off-diagonal entries is 1e-8.R.chr*.3.mat
: the hard threshold for small off-diagonal entries is 1e-3.