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For a project I've been working on, I've been looking at the HapMap Project, and the associated online files. The README file states that for each legend file for each chromosome/region, there is an rs id, an allele coded 0, 1, and a base pair position.

I presume that base pair position means where each nucleotide is located along the genetic sequence. Is this correct?

But what do "rs id" and the other terms mean?

Here's the link to the README file, and in the same directory are the files about the participants, only including SNPs.

HapMap Project README file link

HapMap Project sequence data link (phase 2)

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rs id is reference SNP cluster ID see here. It's basically a unique identifier.

This table is taken from your link:

rs              position        0       1
rs11089130      14431347        C       G  
rs738829        14432618        A       G  
rs915674        14433624        A       G

The allele codes are the 3rd and 4th columns. An SNP is site where a different base is found in different versions of the same gene (different versions of genes are alleles). For a given SNP the different alleles are referred to as the 0 or the 1 allele. So in the table the first SNP, rs11089130, has two alleles: allele 0 has a C at the SNP position (14431347) whereas allele 1 has a G at that position. The allele code does not imply any biological significance.

I'm not sure what would happen if there were three alleles at an SNP, but presumably there would then also be an SNP coded as 2.

Edit: Allele 0 is the residue from the reference genome. Allele 1 is the residue being studied, the SNP.

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  • $\begingroup$ so 0 is the standard allele and 1 is the mutated allele? $\endgroup$
    – higgs241
    Commented Jun 19, 2013 at 16:51
  • $\begingroup$ @higgs241 0 is the residue found in the reference genome and 1 is the residue found in others. Please don't refer to "mutated alleles" variation is the norm... $\endgroup$
    – terdon
    Commented Jun 19, 2013 at 16:56
  • $\begingroup$ @terdon is the reference genome the same for every registered SNP? I mean, if you took the 0 allele at every SNP registered with a rsID, would you end up with the genetic profile of one specific individual? It seems not: I read in en.wikipedia.org/wiki/Reference_genome that "the Genome Reference Consortium human genome (build 37) is derived from thirteen anonymous volunteers from Buffalo, New York". Is that the genome used as a reference for 0/1 labelling of SNPs? And what to do when there is polymorphism in this group of people? Maybe I could make a new question... $\endgroup$
    – bli
    Commented Jun 20, 2013 at 9:13
  • $\begingroup$ @bli It seems pretty clear from the WP page that you link to that the reference genome is a curation construct and so does not correspond to one individual. in fact the page includes this sentence: "The ABO blood group system differs among humans, but the human reference genome contains only an O allele (although the other alleles are annotated)." $\endgroup$
    – Alan Boyd
    Commented Jun 20, 2013 at 14:23
  • $\begingroup$ @Alan Boyd Yes, I should have read the page further. So there is this "GRC human genome (build 37)" which is an artificial haploid reference. Is this the reference for all registered SNP? It could be but I have no certainty. One reason for my doubts is the following: Can it happen that a new SNP is identified in a portion of the genome not yet present in this reference genome? I suspect this is becoming rare, but when this reference was in earlier stages of construction, may be it could have happened. $\endgroup$
    – bli
    Commented Jun 20, 2013 at 16:23

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