ld_matrix

Identifier

pan_ukbb.ld_matrix

Description

Pairwise Pearson correlation (r) of genotypes between variants in the Pan-UKBB LD reference panel.

One row per (ancestry, chromosome, i, j) triple, where i and j index into ld_variants.idx.

One row per variant pair in linkage disequilibrium within an ancestry-specific panel.

Always filter on ancestry and chromosome (partition columns).

Join i or j to ld_variants.idx to attach variant identity. r^2 is the conventional LD measure — square r.

Related tables: pan_ukbb.ld_variants (join on ancestry, chromosome, i, j).

Partitions

• ancestry
  • 'AFR'
  • 'AMR'
  • 'CSA'
  • 'EAS'
  • 'EUR'
  • 'MID'
• chromosome
  • '1'
  • '10'
  • '11'
  • '12'
  • '13'
  • '14'
  • '15'
  • '16'
  • '17'
  • '18'
  • '19'
  • '2'
  • '20'
  • '21'
  • '22'
  • '3'
  • '4'
  • '5'
  • '6'
  • '7'
  • '8'
  • '9'
  • 'X'

Schema

Column	Type	Description
ancestry	TEXT	Partition column. Population ancestry code: AFR = African, AMR = Admixed American, CSA = Central-South Asian, EAS = East Asian, EUR = European, MID = Middle Eastern.
chromosome	TEXT	Partition column. Chromosome on which the variant is located.
i	INT	0-based index of the first variant in the rows/columns of the original LD BlockMatrices.
j	INT	0-based index of the second variant in the rows/columns of the original LD BlockMatrices.
r	FLOAT	The Pearson correlation of genotypes between variants i and j in the given ancestry population.