'Chrom' Field In Ucsc Genome Data

Question

[Russh]

Hi, hope this isn't too simple.

I've been obtaining data about human gene coordinates from UCSC via their mysql system. If I pull out data for most genes, the 'chrom' field returns with self-explanatory values 'chr1' etc.

For NOTCH4 (and presumably for others) I obtain the following values 'chr6apphap1', 'chr6mannhap4', 'chr6msfhap5'... I was wondering what the 'app_hap1' part meant, and, as I can't find any details on the UCSC help page, thought I'd ask here (the extra text messed around with one of my scripts).

All the best, R

Answer 1

[Bert Overduin]

These are the MHC region haplotypes on chromosome 6.

For more info see towards the bottom of this page:

http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=191600823&chromInfoPage=