variants

Identifier

ukb_ppp.variants

Description

Variant annotation table with rsIDs and positional mappings across genome builds.

One row per variant tested for any pQTL association.

Always filter on chromosome (partition column).

Query by variant_id to get the rsID and cross-build positions for a pQTL hit.

Query by rsid to find the UKB-PPP variant_id.

Batch lookups: use variant_id IN (...) to get rsIDs for multiple variants in one query.

Optionally filter by in_dbsnp (variant had a match in dbSNP), was_swapped (beta and effect_allele_frequency were inverted during harmonization), or is_palindromic (alleles are A/T or C/G, should be treated with extra caution due to uncertain inference of strand).

Related tables: ukb_ppp.pqtls (join on variant_id); dbsnp.vcf (join on rsid, chromosome).

Partitions

• 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
variant_id	TEXT	Unique UKB-PPP variant identifier (e.g. 4:180574458:A:G:imp:v1).
rsid	TEXT	dbSNP rsID (e.g. rs123456). May be null for novel variants.
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.
effect_allele	TEXT	Effect allele of pQTL results. Harmonized to equal the dbSNP alt_allele.
other_allele	TEXT	Non-effect allele of pQTL results. Harmonized to equal the dbSNP ref_allele.
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 has a match in dbSNP (allowing for swapping of alleles).
is_palindromic	BOOLEAN	Variant alleles are A/T or C/G. These require specific treatment during harmonization.
was_swapped	BOOLEAN	Effect and other alleles in the source UKB-PPP pQTL files were in the opposite order from dbSNP REF/ALT (on the aligned strand). When true, beta and effect_allele_frequency were inverted during harmonization.
was_flipped	BOOLEAN	Source UKB-PPP pQTL files reported the variant on the reverse strand relative to dbSNP; alleles were reverse-complemented during harmonization. Null for variants without a confident strand assignment.