Bulk searching locus tables (including L2G and V2G data) in Open Targets Genetics using Google BigQuery

Data Access
#1

I am interested in downloading locus tables (see example below) for many genes in bulk. I viewed all tables available in Google BigQuery but I cannot find a database that stores the locus-to-gene data, with the “Overall V2G” scores.

Is there a way to download such tables in bulk, or maybe the whole database, that I could extract genes of interest?

Study ID Study Detail Lead Variant Tag Variant Gene Lead Variant P-value Beta Odds Ratio 95% Confidence Interval Expansion LD (r²) Posterior Probability Overall V2G View
GCST007236 Breast cancer 1_55523741_T_G 1_55520203_G_A ENSG00000169174 3.05E-08 2.708413394 0.63349183 0
FINNGEN_R5_E4_HYPERLIPNAS Hyperlipidaemia other/unspecified 1_55039974_G_T 1_54562566_C_T ENSG00000169174 9.80E-10 0.687220553 0.016756482 0
NEALE2_20002_1224 Thyroid problem (not cancer) non-cancer illness code, self-reported 1_52907888_C_T 1_54553221_T_A ENSG00000169174 7.21E-09 5.561709089 0.001171434 0
…

The table has an additional 2,428 rows

This question was sent to the Open Targets helpdesk and has been posted here so the answer can benefit the whole Community of users.

#2

Hi, seems you already have the V2G scores for these variants/gene assignments. The L2G (can be bulk downloaded via ftp or GCS) is slightly different as it provides gene assignments at a locus level, rather than at a variant level.

A potential solution is to join the L2G table and your input table based on the following columns: study ID (study_id in L2G), lead variant (concat chrom, pos, ref, alt in L2G), Gene (gene_id in L2G).