HaploRegv5

v5 · GRCh38 · 1000 Genomes · 127 epigenomes

Find the variant behind the signal.

A GWAS hit points to a haplotype, not a cause. HaploReg expands each variant to everything in linkage disequilibrium with it, then lines up chromatin state, motif changes, protein binding and trait associations for every candidate.

Simulated linkage disequilibrium across 120 variants. Each line joins pairs the same distance apart, raised by their r², so haplotype blocks stand as plateaus. Drag to turn.

Demo · 2 min 17 s

One locus, start to finish.

rs1421085 at FTO in Classic, then the reimagined Explore and Map & reasoning, then its evidence exported into Mantis as a dense map you can measure and follow back. Every shot is the live site or Mantis itself.

On-screen captions
  1. A GWAS hit points to a haplotype. Not a cause.
  2. 94 variants. Which one does the work?
  3. HaploReg annotates every variant: enhancers, promoters, motifs, eQTLs, chromatin, GWAS hits, conservation.
  4. HaploReg Classic: the table HaploReg v4 users know, rebuilt on GRCh38. Every variant in LD with the query, with r² and D′. Frequencies, regulatory marks, motifs and GWAS hits.
  5. Then, reimagined. Explore: start from a variant, a gene or a region. One query expands to the whole haplotype: 94 variants. Evidence chips filter the block in one click.
  6. Map & reasoning: each variant is placed by its evidence, not its position. The trace shows its work: 94 variants, 7 regulatory. rs11642015 leads by a narrow 0.01. Evidence, not proof.
  7. Export evidence: a row per variant, GWAS hit and enhancer.
  8. Into the same Mantis project, as a second map. 1,143 rows: each variant, GWAS hit and enhancer overlap. Embedded, laid out, clustered and named (4 minutes, 48× in the film).
  9. One project, two maps of the same locus: the 94 variants, and the 1,143 pieces of evidence behind them.
  10. Sem. Ruler measures meaning in the full embedding, not the 2D layout. A BMI hit and a food-liking hit: cos sim 0.73. Two BMI hits, from different variants: cos sim 0.93. Landmarks: one telling point per cluster, chosen by Mantis.
  11. Zoom in on rs11642015: its point keeps every HaploReg field. Its haploreg_url links straight back to that variant's record in HaploReg Explore.
  12. All in one place. HaploReg × Mantis.

Explore

LD plots, a chromatin-state heatmap across 127 epigenomes, and a Mantis-style evidence map with a traced reasoning journey for every locus.

Documentation

Every column, option and term defined, with reference tables for chromatin states, tissues and populations.

Classic

The HaploReg v4 interface on the v5 data layer. The same query form, result tables and text output.