I might be wrong, but could it mean different haplotypes per gene (set)? I mean, I'm looking at the peak at chromosome 6, and if I'm not mistaken, that's where HLA comes in (long story short: HLA is an important family of proteins presenting antigens to CD4+/CD8+ T-lymphocytes (MHC class II type HLA (DR, DQ) and MHC class I type HLA (A, B, C, E are the most important ones), respectively. (If you're wondering: MHC = major histocompatibility complex; the complex of genes on Cx6 of which transcription and subsequent translation results in HLA)
Now, you have to know, that there are much subtypes of HLA. Every single person has a full set of HLA-proteins, and can express 2 types of HLA-A, 2 types of HLA-B, ..., 2 types of HLA-DR, 2 types of HLA-DQ, ...
Why 2 types? Your mother and father have 2 different types themselves, and then there's you, resulting from a combination of 2 of those 4 subtypes.
With subtype, I mean e.g. HLA-DR*0401, HLA-A2 (with different subtypes *020X with X being another number) ... I'm not sure whether I should speak of haplotypes, allotypes, ..., because we've never gotten these terms explained well ...
While we're at it: could someone explain allotype, haplotype?
Well, altogether: there are about 15 000 possible HLA-subtypes. I think that's responsible for the peak. And I think the highest point you see there, is a subtype of HLA-A2. If I'm not mistaken, (a subtype of) HLA-A2 is present in about 50% of the population.
An specific example: people who carry a copy of HLA-DR4 with a specific amino acid configuration (L67,Q70,K/R71 instead of e.g. I67,D70,E71) are at higher risk of developing rheumatoid arthritis (the specific HLA-DR4 subtype is capable of presenting citrullinated proteins - which happen to pop up in every single one of us - to CD4+ T-lympho's, inducing the whole cellular inflammation cascade), though other factors need to be present as well (PTPN22-deficit: the phosphatase won't be able to nib phosphate off of the T-cell receptors (type Trk), leaving it constitutively active for HLA-DR4)
So I think the reason why there's so many variation in number of Y-axis-units here, is the possibility of variation in the presentation of the proteins for which the genes depicted code