POLYMER GENOMICSchr6·hg38·170.8 Mb
Atlas
Open chr6 in viewer Chromosome 6
The immunological chromosome — a 7.6-megabase fortress of genetic diversity at 6p21 that has been under balancing selection for 31 million years, containing more disease-associated variation than the rest of the genome combined.
Physical Properties
Length170.8 Mb
Centromeresubmetacentric
p-arm58.6 Mb
q-arm111.0 Mb
GC content39.6%
Genomic Features
Protein-coding genes1,057
Gene density6.2 / Mb
CpG islands16,338
EPIC v2 probes55,940
Notable
Largest genePARK2 (1.4 Mb)
Disease associations
Type 1 diabetes
Ankylosing spondylitis
Celiac disease
· Contains the MHC/HLA locus — most polymorphic region in the genome
· The HLA complex spans 3.6 Mb with >200 genes
· HLA associations underlie >100 autoimmune diseases
Genomic Architecture
The MHC/HLA super-locus — 7.6 Mb at 6p21.3 containing ~260 expressed genes among 523 total loci in five sub-regions. Most gene-dense and most polymorphic region in the genome.
Long-range LD — Ancestral haplotypes (e.g., A1-B8-DR3) extend across 3+ Mb with little recombination, maintained by selection and suppressed recombination.
Structural DNA variation — Different MHC haplotypes show distinct stacking energy, curvature profiles, and open chromatin patterns.
Evolutionary History
Centromere repositioning — Ancestral centromere at 6p22.1 relocated to current position 17-23 Mya. A human neocentromere was discovered at the exact ancestral position — "centromere memory" persisting for 17+ million years.
MHC antiquity — Recognizable organization appears with jawed vertebrates ~450 Mya. Shark MHC already contains class I and II genes.
Deep Cuts
Your HLA may be older than your species — Two humans can differ more at HLA-DQB1 than a human and a baboon sharing the same ancestral lineage. Among the oldest known examples of balancing selection.
The autoimmune haplotype — A1-B8-DR3 extends 3+ Mb and is associated with virtually every autoimmune disease. Carried by ~8% of Northern Europeans.
The centromere ghost — A neocentromere jumped back to 6p22.1 — where the ancestral centromere sat 17-23 Mya. "Centromere-forming potential" persisted across millions of years.
§ Deep dive