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  • Phase output blocks

  • See corresponding data for another gene
Haplotype Frequency Sort Order
Haplotype All Controls Cases
GT
1630 81.6% 808 81.8% 822 81.4%
AC
270 13.5% 129 13.1% 141 14.0%
AT
97 4.9% 51 5.2% 46 4.6%
GC
01 0.1% 00 0.0% 01 0.1%
Totals
1998 988 1010

Haplotype Alphabetic Sort Order
Haplotype All Controls Cases
AC
270 13.5% 129 13.1% 141 14.0%
AT
97 4.9% 51 5.2% 46 4.6%
GC
01 0.1% 00 0.0% 01 0.1%
GT
1630 81.6% 808 81.8% 822 81.4%
Totals
1998 988 1010
Minimal SNP (highlighted columns) needed to unambiguously distinguish haplotypes seen more than once, by population group
Please note that this an experimental resource which is still under test.Please email Ross Lazarus if you have comments or find any errors or anomalies

Minimal sets of haplotype tagging SNP for CCL5 in Cases

The following SNP are binary equivalent. Any one of them may be freely substituted for any of the others without any loss of ability to distinguish haplotypes:
SNP 1 may be substituted by any of 2, 3

1 2 3 #
8 2 2 (822)
1 4 1 (141)
Legend:
  • Same allele as first row of the corresponding SNP column    
  • Variant allele:    

Minimal sets of haplotype tagging SNP for CCL5 in Controls

The following SNP are binary equivalent. Any one of them may be freely substituted for any of the others without any loss of ability to distinguish haplotypes:
SNP 1 may be substituted by any of 2, 3

1 2 3 #
8 0 8 (808)
1 2 9 (129)
Legend:
  • Same allele as first row of the corresponding SNP column    
  • Variant allele:    
The haplotypes shown above are comprised of alleles at the following SNP locations in the order show. The first column is the allele position in the haplotype. The SNP column is the SNP position in the reference sequence (1=first base). The RelativeOffset column is the SNP offset relative to the ATG start codon.
#SNPRelativeOffset
14598-471
25375306
*
The PHASE software package was used to generate the contents of this output file. Custom written Python scripts (available on request) were used to create the input files for PHASE (from the raw data files in SeattleSNPs "prettybase" format available elsewhere on this site) and also to process the PHASE output into more useful formats. PHASE uses MCMC methods and is available from http://www.stats.ox.ac.uk/mathgen/software.html . The results were obtained by running PHASE independently for each of the separate groups shown and amalgamating the results. 		 
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