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 Name
  • Allele1: The 1st Allele (hg19 + strand)
  • Allele2: The 2nd Allele (hg19 + strand)
  • Freq.Allele1.HapMapCEU: The Allele Frequency of Allele1 in the HapMap CEU Population
  • b: Estimated Single-SNP Effect Size
  • SE: Standard Error
  • p: Single-SNP P-value
  • N: Sample Size
  • pos: 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.