ChickenGTEx Atlas Home
Data
Overview Resources Download
Molecular Phenotype
Protein-coding Gene Expression Exon Expression LncRNA Expression 3’UTR Alternative Polyadenylation Alternative Splicing Variation
QTL
Cis-molQTL
eQTL exQTL lncQTL 3'aQTL sQTL
Fine-mapping molQTL
eQTL exQTL lncQTL 3'aQTL sQTL
Context-dependent molQTL
Epigenetic Data Single Cell TWAS IGV
Help
Documentation Contact / Join Us
chickenGTEx ChickenGTEx Atlas
Home
Data
Overview Resources Download
Molecular Phenotype
Protein-coding Gene Expression Exon Expression LncRNA Expression 3’UTR Alternative Polyadenylation Alternative Splicing Variation
QTL
Cis-molQTL
eQTL exQTL lncQTL 3'aQTL sQTL
Fine-mapping molQTL
eQTL exQTL lncQTL 3'aQTL sQTL
Context-dependent molQTL
Epigenetic Data Single Cell TWAS IGV
Help
Documentation Contact / Join Us
chickenGTEx chickenGTEx

ChickenGTEx Atlas

As an essential part of the ongoing Farm animal Genotype-Tissue Expression (FarmGTEx) project, the ChickenGTEx Atlas aims to build a comprehensive public catalogue of genetic regulatory variants associated with multiple types of transcriptomic phenotypes in distinct biological contexts (e.g., tissues, cell types, development periods, gender, environmental exposures, and genetic backgrounds) in chickens. This resource will serve as a valuable reference for fundamental biology (e.g., genetic regulations related to development, immune response, and tissue/cell type specificity), bird or vertebrate evolution, comparative transcriptomes, applied genetics (e.g., chicken precision breeding, and food security), and human biomedicine.

Exploring the ChickenGTEx atlas by variants, genes, and tissues

WGS Data
2,869
RNA-Seq Data
7,015
Tissues
52
Molecular Phenotypes
5
Epigenetic Data
257
Single Cells
203,540
Associations
22,148,859
Gene Expression
Cis-eQTL
Exon Expression
Cis-exQTL
lncRNA Expression
Cis-lncQTL
3'UTR APA
Cis-3'aQTL
Alternative Splicing
Cis-sQTL
Single cell Expression
Context-dependent Cis-eQTL

Please cite:   The ChickenGTEx portal: a pan-tissue catalogue of regulatory variants shaping transcriptomic and phenotypic diversity. Nucleic Acids Research, 2025.

Publications

Genetic regulation of gene expression across multiple tissues in chickens.
Nat Genet. 2025. DOI:10.1038/s41588-025-02155-9
An atlas of regulatory elements in chicken: A resource for chicken genetics and genomics.
Science Advance. 9, eade1204 (2023). DOI:10.1126/sciadv.ade1204
The CattleGTEx atlas reveals regulatory mechanisms underlying complex traits
Nature Genetics, 54, 1273-1274 (2022), DOI: 10.1038/s41588-022-01155-3
Comparative transcriptome in large-scale human and cattle populations
Genome Biology, 23, 176 (2022), DOI: 10.1186/s13059-022-02745-4
A multi-tissue atlas of regulatory variants in cattle
Nature Genetics, 54, 1438–1447 (2022), DOI: 10.1038/s41588-022-01153-5
The conservation of human functional variants and their effects across livestock species
Communications Biology, 5, 1003 (2022), DOI: 10.1038/s42003-022-03961-1
Pig genome functional annotation enhances the biological interpretation of complex traits and human disease
Nature Communications, 12, 5848 (2021), DOI: 10.1038/s41467-021-26153-7
A compendium of genetic regulatory effects across pig tissues.
bioRxiv, 2022, DOI: 10.1101/2022.11.11.516073
Genetic score omics regression and multi-trait meta-analysis detect widespread cis -regulatory effects shaping bovine complex traits
bioRxiv, 2022, DOI: 10.1101/2022.07.13.499886
Gene expression and RNA splicing explain large proportions of the heritability for complex traits in cattle
bioRxiv, 2022, DOI: 10.1101/2022.05.30.494093
Building an atlas of transposable elements reveals the extensive roles of young SINE in gene regulation, genetic diversity, and complex traits in pigs
bioRxiv, 2022, DOI: 10.1101/2022.02.07.479475

News and Events

2025-03-15
The ChickenGTEx Atlas is now available online.
2025-02-21
Download open access GWAS results for complex traits.
2024-08-12
Visualize gene expression & cell types in single-cell data.
2023-01-10
Developmental gene expression data contribution to phase 1.
2023-01-10
Sing-cell sequencing data contribution to phase 1.
2023-01-09
RNA-Seq data contribution to phase 1.
2023-01-03
WGS data contribution to phase 1.
2022-10-31
The pilot phase of ChickenGTEx resources release.
2022-10-01
The phase 1 of ChickenGTEx is starting.
Copyright © the FarmGTEx-ChickenGTEx Consortium.
It is developed and maintained by CNCB-NGDC. To provide feedback or ask a question, contact us on chickengtex(AT)farmgtex.org