Bulk PheWAS data download

Technical Support
1

Hello,
I’m a beginner for accessing and utilizing GWAS / PheWAS data.
I’d like to operate meta-analysis of PheWAS & GWAS data from various biobanks in order to achieve more significant PheWAS & GWAS data.
Could I get total PheWAS data of whole variants detected?

In the case of PheWAS, each summary statistics about just one variant from various studies could be shown in web interface for each studies.

2

Hi Jisu!

Welcome to the Open Targets community and thank you for your interest in our resource!

In terms of our PheWAS results, we collect for each variant (say, V1) all GWAS association statistics where V1 appears, whether significant or not. This constitutes the PheWAS plot seen in the Open targets genetics variant page.

Hence, if you would like to collect the association statistics for a set of variants of interest, you could either use the GraphQL API (see example below), or access the bigQuery SQL table (variant_disease table).

Example query to return all associations for variant “1_154453788_C_T” :

query Variant {
  tagVariantsAndStudiesForIndexVariant(variantId: "1_154453788_C_T") {
    associations {
      tagVariant {
        id
        rsId
        __typename
      }
      study {
        studyId
        traitReported
        __typename
      }
      pval
      beta
      __typename
    }
    __typename
  }
}

Best wishes,
Xiangyu

3

Hi, Xiangyu!

Thank you for helping me.
Could I get Bulk PheWAS and GWAS data file from FTP server?
or Could I get Variant metadata with significant target genes(based on eQTL) from FTP?

Have a nice day!

4

Hi Jisu,

You can find them under the ”sa/“ directory in the ftp downloads.

Best wishes,
Xiangyu

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