DOI: 10.5281/zenodo.14982207
title: mRNA expression quantitative trait loci used in the manuscript titled: MR-link-2: pleiotropy robust cis Mendelian randomization validated in three independent reference datasets of causality

description: # eQTLGen Data for MR-link-2This repository contains 54 Parquet files generated by the eQTLGen Consortium. These datasets were used in the [MR-link-2 paper]() to identify the correct direction of causality.---## Important Disclaimer- **These data are provided for reproducing the results of the MR-link-2 paper.**- There is an **upcoming publication** from the eQTLGen Consortium that will feature **larger sample sizes** and **additional gene expression phenotypes**. If you require more comprehensive datasets, please refer to the forthcoming publication once it is available.---## Files Overview- **Number of files:** 54  - **Format:** Parquet  - **Content:** Cell-type marker gene eQTL data generated by the eQTLGen Consortium  - **Harmonization:** Each file has been harmonized to the UK10K genotype reference and is in b37  ---## Data FormatThe Parquet files follow the **GWAS format specification**, which also makes them compatible with the MR-link-2 method. The schema of each file is as follows:```plaintextchromosome              | stringbase_pair_location      | uint64effect_allele           | stringother_allele            | stringbeta                    | float64standard_error          | float64effect_allele_frequency | float64p_value                 | float64variant_id              | stringrsid                    | stringn                       | uint64```**Field Descriptions:**- **chromosome**: The chromosome on which the variant is located (e.g., "1", "2", "X").  - **base_pair_location**: The base pair position of the variant on the chromosome.  - **effect_allele**: The allele for which the effect size (`beta`) is reported.  - **other_allele**: The non-effect allele.  - **beta**: The estimated effect size of the effect allele on the gene expression.  - **standard_error**: The standard error of the effect size estimate.  - **effect_allele_frequency**: The frequency of the effect allele in the reference dataset (UK10K).  - **p_value**: The p-value for the association.  - **variant_id**: A unique identifier for the variant (often in the format `chr:pos:ref:alt`).  - **rsid**: The dbSNP rs identifier (if available).  - **n**: The sample size for the specific variant-gene association.------## Getting Started1. **Dependencies**:     - A Parquet-reading library (e.g., [pyarrow](https://arrow.apache.org/docs/python/) in Python) to load these files.   - Any standard GWAS/QTL analysis tool or MR-link-2 method pipeline.2. **Loading Example (Python)**:   ```python   import pyarrow.parquet as pq   # Example: load the first Parquet file   file_path = "eqtlgen_marker1.parquet"   table = pq.read_table(file_path)   df = table.to_pandas()   # Inspect the first few rows   print(df.head())   ```3. **Analysis**:     - After loading, the data can be integrated into your pipelines for QTL mapping, colocalization studies, or Mendelian randomization analyses with MR-link-2.---## Contact and SupportIf you have any questions regarding the usage or interpretation of these datasets in the context of MR-link-2:- **MR-link-2 Support**: [https://github.com/adriaan-vd-graaf/mrlink2](https://github.com/adriaan-vd-graaf/mrlink2)Please direct inquiries about the upcoming eQTLGen dataset to the eQTLGen Consortium.