Innate Immunity in Heart, Lung and Blood Disease
Programs for Genomic Applications
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Related documents:
- Phase output blocks
- See corresponding data for another gene
| Haplotype counts inferred by Phase*. |
| Gene = IL17F, Minimum allele freq. in ANY population= 0.000, 5 SNP, 1027 Subjects |
| Note that the haplotypes shown below comprise 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 Gene transcription start codon. |
| # | SNP | RelativeOffset |
| 1 | 6166 | 1165 |
| 2 | 7368 | 2367 |
| 3 | 12470 | 7469 |
| 4 | 12489 | 7488 |
| 5 | 13063 | 8062 |
| Haplotype Frequency Sort Order | |||||||
| Haplotype | All | Controls | Cases | ||||
| TTGAG | 845 | 41.1% | 447 | 43.3% | 398 | 38.9% | |
| CCGAG | 487 | 23.7% | 230 | 22.3% | 257 | 25.1% | |
| TCGAG | 383 | 18.6% | 186 | 18.0% | 197 | 19.3% | |
| TCGAC | 178 | 8.7% | 93 | 9.0% | 85 | 8.3% | |
| TTGGG | 86 | 4.2% | 43 | 4.2% | 43 | 4.2% | |
| CCAAG | 71 | 3.5% | 32 | 3.1% | 39 | 3.8% | |
| CCGGG | 02 | 0.1% | 00 | 0.0% | 02 | 0.2% | |
| TTGAC | 01 | 0.0% | 00 | 0.0% | 01 | 0.1% | |
| TCGGG | 01 | 0.0% | 01 | 0.1% | 00 | 0.0% | |
| Totals | 2054 | 1032 | 1022 | ||||
| Haplotype Alphabetic Sort Order | |||||||
| CCAAG | 71 | 3.5% | 32 | 3.1% | 39 | 3.8% | |
| CCGAG | 487 | 23.7% | 230 | 22.3% | 257 | 25.1% | |
| CCGGG | 02 | 0.1% | 00 | 0.0% | 02 | 0.2% | |
| TCGAC | 178 | 8.7% | 93 | 9.0% | 85 | 8.3% | |
| TCGAG | 383 | 18.6% | 186 | 18.0% | 197 | 19.3% | |
| TCGGG | 01 | 0.0% | 01 | 0.1% | 00 | 0.0% | |
| TTGAC | 01 | 0.0% | 00 | 0.0% | 01 | 0.1% | |
| TTGAG | 845 | 41.1% | 447 | 43.3% | 398 | 38.9% | |
| TTGGG | 86 | 4.2% | 43 | 4.2% | 43 | 4.2% | |
| Totals | 2054 | 1032 | 1022 | ||||
Minimal SNP (loci shown in red) 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 IL17F in Cases
Note: Blue = same allele as first row of the corresponding SNP column; Red = variant allele
| 0 | 0 | 1 | 1 | 1 | |
| 6 | 7 | 2 | 2 | 3 | |
| 1 | 3 | 4 | 4 | 0 | # |
| 6 | 6 | 7 | 8 | 6 | |
| 6 | 8 | 0 | 9 | 3 | |
| T | T | G | A | G | (398) |
| C | C | G | A | G | (257) |
| T | C | G | A | G | (197) |
| T | C | G | A | C | (85) |
| T | T | G | G | G | (43) |
| C | C | A | A | G | (39) |
| C | C | G | G | G | (2) |
Minimal sets of haplotype tagging SNP
for IL17F in Controls
Note: Blue = same allele as first row of the corresponding SNP column; Red = variant allele
| 0 | 0 | 1 | 1 | 1 | |
| 6 | 7 | 2 | 2 | 3 | |
| 1 | 3 | 4 | 4 | 0 | # |
| 6 | 6 | 7 | 8 | 6 | |
| 6 | 8 | 0 | 9 | 3 | |
| T | T | G | A | G | (447) |
| C | C | G | A | G | (230) |
| T | C | G | A | G | (186) |
| T | C | G | A | C | (93) |
| T | T | G | G | G | (43) |
| C | C | A | A | G | (32) |
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.