About & Data

Pseudogenomes for 1135 Arabidopsis thaliana strains were generated by combining reference and variant calls including deletions, with uncalled sites represented as Ns.

Data & Downloads

The data powering SNPst☆r is published as an Annotated Research Context (ARC) — Arabidopsis thaliana GWAS & Proteotype ARC (export 2026-06-05, 38.2 GB total).

Recommended: download the complete ARC (all datasets, ISA metadata and documentation in one bundle) from the repository: Open the ARC repository »

Or download individual collections directly. All collections are gzipped JSON Lines (one document per line) except the SNP catalog, which is gzipped BSON (mongodump) and is restored with mongorestore, and the derived CDS/InterPro table, which is gzipped CSV. See the README and METADATA documents for details. The two derived Cys → Trp variant lists are plain CSV and open directly in a spreadsheet.

Climate-factor GWAS (study)

Dataset	Documents	Size	Format	sha256
Climate-factor GWAS (raw p-values) Raw GWAS p-values per SNP across ~196 climate factors. Climate-factor keys join to climate_factors_upd for human-readable descriptions.	3,042,994	250 MB	`jsonl.gz`	`ce9831a2c6c5…`	↓ Download
Climate-factor GWAS (enriched p<1 subset) Enriched subset of GWAS hits with p<1; climate-factor sub-documents carry pval, description and link inline.	185,450	12 MB	`jsonl.gz`	`ccc12893ee6c…`	↓ Download
Climate-factor descriptions Canonical descriptions of the ~196 climate factors (ID, Description, Link, Source, Units).	196	6.2 KB	`jsonl.gz`	`c2e256803d60…`	↓ Download
Climate-factor key → human-id join Join table mapping machine GWAS keys (actualID) to human-readable ID, Description, Link, Source and Units.	195	7.2 KB	`jsonl.gz`	`97ba41c0969a…`	↓ Download

Ferrero-Serrano Á, Assmann SM (2019). Nat. Ecol. Evol. 3, 274-285. doi:10.1038/s41559-018-0754-5

AraGWAS Catalog (study)

Dataset	Documents	Size	Format	sha256
AraGWAS significant hits Curated significant SNP×phenotype associations from the AraGWAS Catalog (snp_id_c, chr, position, score, maf).	36,399	1.3 MB	`jsonl.gz`	`ef77e7a85371…`	↓ Download

Togninalli M et al. (2018). Nucleic Acids Res. 46(D1), D1150-D1156. doi:10.1093/nar/gkx954

SNP, haplotype, proteotype & structure assays

Dataset	Documents	Size	Format	sha256
SNP catalog Full SNP catalog used by the website (transcript_id, snp_id, snp_dp, snp_location, ...). Gzipped BSON; restore with mongorestore. Large file (≈11 GB) — the complete ARC is the recommended way to obtain it.	20,010,332	11 GB	`bson.gz`	`a0405c535f8e…`	↓ Download
Haplotypes Per-transcript haplotypes across accessions (haplotype_id, haplotype_number, num_snps, num_accessions).	6,348,060	685 MB	`jsonl.gz`	`b3ed98041a72…`	↓ Download
Transcript regions Transcript genomic regions (transcript_id, chr, strand, start, end).	52,060	219 MB	`jsonl.gz`	`bf148c32fad1…`	↓ Download
Proteotype haplotypes Protein-level haplotype groups (transcript_id, protein_haplotype_id, protein_haplotype_number, num_accessions, accessions).	3,495,265	422 MB	`jsonl.gz`	`488ebe820857…`	↓ Download
Proteotype structures AlphaFold/PDB structural data per proteotype (transcript_id, proteotype_id, pdb_structure, filename, file_path). Very large file (≈26 GB) — the complete ARC is the recommended way to obtain it.	356,807	26 GB	`jsonl.gz`	`1fd5cd88c2a9…`	↓ Download
ThermoMPNN stability predictions ThermoMPNN ΔΔG stability predictions per protein (uniprot_id, protein_length, predictions, source_file, model_version).	41,597	1.3 GB	`jsonl.gz`	`abba4ef25900…`	↓ Download
CDS variants with InterPro / domain annotation (derived) One row per non-reference CDS SNP (snp_location = CDS, snp_is_ref = no): transcript_id, snp_id_c, aa_pos, and the InterPro entries and InterProScan signatures hit at that amino-acid position. Derived from snp_29_11_2024 by matching aa_pos against protein_domains_interproscan.regions_protein in regions_01_12_2025 — the same rule the SNP table applies. Multiple hits are separated by ';' and IDs stay aligned with their descriptions.	3,822,870	23 MB	`csv.gz`	`de19cb455410…`	↓ Download
Cys → Trp missense variants (derived) Every record shown as "Cys -> Trp" in the SNP table's "Amino acid substitution" column, across all transcripts (all 1135 accessions, default cutoffs). One row per transcript isoform, with the SNP table's own columns: SNP_ID, base frequencies, amino-acid and mRNA position, SNP location and effect, substitution, chemical-property effect, ThermoMPNN ΔΔG, impact annotation, InterPro ID and description, AraGWAS top hits and climate-factor GWAS hits. Derived from snp_29_11_2024 by selecting snp_aa_seq = "Cys -> Trp" with snp_aa_change = nonsynonymous.	2,500	451 KB	`csv`	`0523bfe10ff6…`	↓ Download
Cys → Trp missense variants, splice-region subset (derived) Companion to the table above: records stored as "Cys -> Trp" in snp_29_11_2024 whose snp_aa_change is missense_variant&splice_region. The SNP table leaves the "Amino acid substitution" cell empty for these, so they are not reachable by filtering that column. Same columns, plus a Note column.	22	7.5 KB	`csv`	`1b3172c70724…`	↓ Download

Derived from the 1001 Genomes panel — 1001 Genomes Consortium (2016). Cell 166, 481-491. doi:10.1016/j.cell.2016.05.063

Cross-assay lookup tables

Dataset	Documents	Size	Format	sha256
Accession data Accession metadata (acc_id, name, cs_number, country, group).	1,135	18.5 KB	`jsonl.gz`	`5d58eb9473b8…`	↓ Download
Accession locations Geolocations per accession (accession_id, name, lat, lng, country).	7,406	87 KB	`jsonl.gz`	`9aaaed3d36aa…`	↓ Download
Transcript → UniProt mapping Mapping between transcripts and UniProt entries (uniprot_id, isoform_id, gene_name).	48,321	778 KB	`jsonl.gz`	`0ed018b664b0…`	↓ Download

Accession metadata derived from the 1001 Genomes panel (Cell 2016, 166, 481-491).

Programmatic data access (API)

The full Arabidopsis thaliana / 1001 Genomes GWAS dataset can be accessed programmatically through the public AraGWAS REST API: https://aragwas.1001genomes.org/api/.

If you use this resource, please cite snpStar. The Collaborative Research Centre CRC 1664 is funded by Deutsche Forschungsgemeinschaft (DFG).

Credits

Pseudogenomes (download FASTA files from the 1001 Genomes Data Center) were generated by Alexander Platzer.
GWAS analysis was performed by Francesco Pezzini with the software GEMMA . Every climate factor was used as a phenotype and for every climate factor, one analysis run was carried out. In a data preprocessing step ecotypes related to missing values were filtered out from the phenotype vector. Minor allele frequency (MAF) and linkage disequilibrium (LD) thresholds in GEMMA were set to 1% and 0.8 respectively. This means only SNPs with a MAF of 1% or high were analysed. The obtained P-values were corrected for multiple comparisons using the Benjamini-Yekutieli method. The climate factor data was taken from the paper by Ferrero-Serrano and Assmann.
The de-novo GWAS are computed with TASSEL 5.0 (https://tassel.bitbucket.io/).
The analysis of the SNP data was performed by Lasse Feldhahn .
This tool was built on the basis of the 1001 Genomes Tool Pseudogenomes ( Github page) developed by Joffrey Fitz.
The additional web app and database development was done by Benjamin Schmidt. The webapp uses bootstrap, selectize, jquery, popper the calipho-sib feature-viewer and sequence-viewer and the webix datatable .
Additional features and enhancements, including the public API and API integration, were developed by Muhammad Tahir.

References

1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana 1001 Genomes Consortium Cell (2016), 166(2) 481-91.
Angel Ferrero-Serrano, Sarah Mary Assmann: Phenotypic and genome-wide association with the local environment of Arabidopsis: Source of the climate factors used for the gwas analysis.

Specify a transcript identifier or gene name:

Select a set of accessions:

Results: AT4G30120.1

HMA3: Heavy metal atpase 3; ATHMA3: A. THALIANA HEAVY METAL ATPASE 3

Compare Proteotypes:

Map of all haplotypes

Map of all proteotypes

Select a set of parameters to filter/sort the SNP data: