SingleBrain: Single-nucleus Trans Expression QTL Meta-analysis Summary Statistics across Multiple Human Brain Cohorts

https://github.com/RajLabMSSM/SingleBrain

Bonferroni significant association summary statistics for trans-eQTLs mapped in a meta-analysis across multiple human brain single-nucleus RNA seq cohorts, as part of the "SingleBrain" project.

Sample size = 983 European ancestry donors from 757 unique donors

4 cohorts (Fujita et al., Mathys et al., Bryois et al., Gabitto et al.) meta-analyzed using the linear mixed model random-effects meta-analysis software mmQTL (PMID: 35058635).

Number of tested SNPs = 265,814

Bonferroni threshold = 0.05/(#genesTested x #variantsTested)

Each file has the following naming convention:

{Cell type}_trans_eqtl_peak_1_sig_assoc.tsv.gz

References

The following reference was used for mapping phenotypes:

1. GENCODE - GENCODE v38 comprehensive transcripts (https://www.gencodegenes.org/human/release_38.html)

Cell type

The following brain 6 major cell types were tested for genetic association:

• Ast: astrocytes
• Ext: excitatory neurons
• IN: inhibitory neurons
• MG: microglia
• OD: oligodendrocytes
• OPC: oligodendrocyte progenitor cell

All phenotype matrices were scaled and centered and then quantile normalized.

Data dictionary

feature: the phenotype being tested

variant_id: the genetic variant being tested

chr: chromosome

pos: position (hg38)

ref: reference allele

alt: alternate allele

fixed_beta: Fixed effect meta-analysis estimate of the beta

fixed_sd: Fixed effect meta-analysis standard error of the beta

fixed_z: Fixed effect meta-analysis Z-score

Fixed_P: Fixed effect meta-analysis P-value

Random_Z: Random effect meta-analysis Z-score

Random_P: Random effect meta-analysis P-value

cis_feature: cross-mappable gene pair with feature

crossmap: cross-mappable gene pairs estimated using Saha et al.[PMID: 30613398]  are filtered less than 5.