ld_scores

Identifier

pan_ukbb.ld_scores

Description

Per-variant LD scores for the Pan-UKBB LD reference panel.

The LD score of a variant is the sum of bias-corrected r^2 estimates with every other variant in its local LD region in the given ancestry population, computed with the LDSC unbiased r^2 estimator; under no LD the expected score is zero, so individual scores can be slightly negative.

One row per (ancestry, variant).

Always filter on ancestry and chromosome (partition columns).

Use variant_id to join to ld_variants.

Higher ld_score indicates a variant in a denser local LD block.

Related tables: pan_ukbb.ld_variants (join on ancestry, chromosome, variant_id); dbsnp.vcf (join on rsid, chromosome).

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.
position_grch37	INT	Variant position in assembly GRCh37 coordinates.
position_grch38	INT	Variant position in assembly GRCh38 coordinates.
ref_allele	TEXT	Forward strand reference allele in assembly GRCh38. Aligned to dbSNP reference allele when variant is present in dbSNP.
alt_allele	TEXT	Forward strand alternate allele in assembly GRCh38. Aligned to dbSNP alternate allele when variant is present in dbSNP.
variant_id	TEXT	Colon-delimited variant identifier in source coordinates: chromosome:position_grch37:ref_allele:alt_allele.
rsid	TEXT	Unique NCBI variant identifier (e.g. rs123456, rs7412). Non-rsid values found in the rsid field of the source table (e.g. “21:9553285_TGA_T”) are set to missing.
ld_score	FLOAT	Pan-UKBB LD score for the variant in the given ancestry population — the sum of bias-corrected r^2 estimates with all other variants in the local LD region. Computed with the LDSC unbiased r^2 estimator (r^2_obs - (1 - r^2_obs) / (N - 2)) so that the expected score under no LD is zero; individual scores can therefore be slightly negative for variants in low-LD regions.
dbsnp_build	TEXT	dbSNP build version that the variant was harmonized against (e.g. b157). Null for variants without a dbSNP match.
in_dbsnp	BOOLEAN	Variant found in dbSNP (matching chromosome and position, and ref_allele and alt_allele matching in some combination).
is_palindromic	BOOLEAN	Variant alleles are A/T or C/G. These require specific treatment during harmonization due to ambiguous strand inference.
was_swapped	BOOLEAN	ref_allele and alt_allele were swapped to align with dbSNP.
was_flipped	BOOLEAN	Variant strand was flipped during liftover from assembly GRCh37 to assembly GRCh38. ref_allele and alt_allele were aligned to forward strand of GRCh38 by taking the reverse complement of the alleles reported in the source.