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ld_variants

Identifier

Section titled “Identifier”
pan_ukbb.ld_variants

Description

Section titled “Description”

Variant catalogue for the Pan-UKBB LD reference panel.

Lists every variant included in an ancestry-specific LD matrix, with its row/column index (idx) in the source BlockMatrix and dbSNP alignment provenance.

One row per (ancestry, variant).

Always filter on ancestry and chromosome (partition columns).

Use idx to look up pairwise correlations in ld_matrix (join idx to either ld_matrix.i or ld_matrix.j within the same (ancestry, chromosome)).

Filter to in_dbsnp = True and is_palindromic = False to drop strand-ambiguous variants.

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

Partitions

Section titled “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

Section titled “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.
alt_allele_frequency FLOAT Frequency of the alternate allele in the ancestry group.
idx INT 0-based index of the variant in the rows/columns of the original LD BlockMatrices.
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.