variants

Identifier

eqtlgen.variants

Description

Harmonised variant catalogue for the eQTLGen meta-analysis.

Provides genotype counts and dbSNP alignment provenance for every variant contributing to eqtls.

One row per variant.

Always filter on chromosome (partition column).

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

Use rsid as the dbSNP lookup key.

Related tables: eqtlgen.eqtls (join on variant_id, chromosome); 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'

Schema

Column	Type	Description
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 eQTL results. Harmonized to equal the dbSNP alt_allele.
other_allele	TEXT	Non-effect allele of eQTL results. Harmonized to equal the dbSNP ref_allele.
variant_id	TEXT	Unique variant identifier within the study. Format is chromosome:position_grch37:AlleleA:AlleleB, where AlleleA is the other_allele before harmonization and AlleleB is the effect_allele before harmonization.
rsid	TEXT	dbSNP rsID (e.g. rs123456). May be null for novel variants.
effect_allele_frequency	FLOAT	Frequency of the effect allele in the study population (excluding the Framingham Heart Study cohort).
n_hom_effect	INT	Total count of genotypes homozygous for effect_allele.
n_hom_other	INT	Total count of genotypes homozygous for other_allele.
n_het	INT	Total count of heterozygous genotypes.
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 files were in the opposite order from dbSNP REF/ALT (on the aligned strand). When true, allele-frequency and effect-direction fields were inverted during harmonization.
was_flipped	BOOLEAN	Source 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.