📋 JoGo Updates & Release Notes

Current Version: JoGo v1.0 — 2025-08-13

v1.0 Released on 2025-08-13

What’s new in v1.0

  • ACTG haplotype catalog & unified IDs (A/C/T/G and combined AC/ACT/ACTG)
  • Search & filters by gene, genic region, and variant
  • Haplotype Explorers: Online (browser) & Local (IGV integration)
  • Integrations with GTEx, ClinVar, and GWAS Catalog
  • Haplotype QTL dataset from three studies (refer below)
  • Downloads & exports (FASTA, JSON)

Data snapshot (v1.0)

Reference

  • MANE release 1.2 (2023-07-21)
  • Samples: 258
  • Genes: 19,194

Haplotype counts (single levels)

  • A (Amino acids): 174,376
  • C (Coding): 300,610
  • T (Transcript): 486,288
  • G (Genebody): 3,695,204

Haplotype counts (combined)

  • AC: 300,610
  • ACT: 784,577
  • ACTG: 3,832,273

Note: AC count equals the number of unique C-level sequences; A is deterministically derived from C.

External annotation snapshots

ClinVar

Version: clinvar_20250715.vcf.gz (retrieved 2025-07-15)

GWAS Catalog

Dataset retrieved 2025-07-17

GTEx

Release v10

Haplotype QTL dataset (v1.0)

Associations are reported for three independent LCL RNA-seq studies, requiring concordant effect directions across all three: Taylor et al. (n=731; 731LCL), Lappalainen et al. (n=462; 462LCL), Ueda et al. (n=87; LCL87JP).

−log10(p) threshold A C T AC ACT Total
242,277100,741165,90599,942241,254650,119
316,43433,59447,27333,45765,750196,508
48,69316,26520,94816,09727,88989,892
55,4889,50211,5889,41314,86950,860
63,8836,3557,2766,2848,92832,726
72,8044,4855,0644,4245,95022,727
82,1733,3273,6423,3284,25216,722
91,6252,5442,7682,5143,12812,579
101,3302,0202,0802,0132,3639,806
Total84,707178,833266,544177,472374,3831,081,939

Selection requires concordant effect directions among all three studies.

Features

Core

  • Advanced search & filters (gene / genic region / variant)
  • Haplotype Explorers (Online & Local with IGV)
  • Population frequency views
  • Haplotype QTL: three studies integrated

Integrations & Exports

  • Annotations: ClinVar / GTEx / GWAS Catalog
  • Exports: FASTA, JSON

Development Updates & Contact

JoGo is actively developed. We welcome community feedback and collaboration.

  • Bug reports: Please submit via our contact page.
  • Feature requests: Suggestions are welcome via our contact page.
  • Collaboration requests: For research or data integration, reach out through the contact page.