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  • Phase output blocks

  • See corresponding data for another gene
Haplotype Frequency Sort Order
Haplotype All Controls Cases
AGCC
539 26.6% 288 27.9% 251 25.3%
ACGT
479 23.6% 320 31.0% 159 16.0%
AGGT
444 21.9% 155 15.0% 289 29.1%
TGGT
426 21.0% 209 20.3% 217 21.8%
AGGC
134 6.6% 58 5.6% 76 7.6%
AGCT
04 0.2% 02 0.2% 02 0.2%
Totals
2026 1032 994

Haplotype Alphabetic Sort Order
Haplotype All Controls Cases
ACGT
479 23.6% 320 31.0% 159 16.0%
AGCC
539 26.6% 288 27.9% 251 25.3%
AGCT
04 0.2% 02 0.2% 02 0.2%
AGGC
134 6.6% 58 5.6% 76 7.6%
AGGT
444 21.9% 155 15.0% 289 29.1%
TGGT
426 21.0% 209 20.3% 217 21.8%
Totals
2026 1032 994
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 CCL2 in Cases

2 4 4 5  
9 1 7 9 #
3 4 1 7  
4 4 0 2  
A G G T (289)
A G C C (251)
T G G T (217)
A C G T (159)
A G G C (76)
A G C T (2)
Legend:
  • Same allele as first row of the corresponding SNP column    
  • Variant allele:    

Minimal sets of haplotype tagging SNP for CCL2 in Controls

2 4 4 5  
9 1 7 9 #
3 4 1 7  
4 4 0 2  
A C G T (320)
A G C C (288)
T G G T (209)
A G G T (155)
A G G C (58)
A G C T (2)
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
12934-2138
24144-928
34710-362
45972900
*
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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