1. What is the name of haploview format to use in this analysis?
2. Show the marker and individual quality control of the genotype data use in the analysis?
3. Show the LD map then explain what do you get from the LD map?
4. How many haplotype blocks in this region of Chromosome X, then explain how to interpret them?
5. Find out the tagging SNP in each haplotype block, then explain what the tagging SNPs?
Open Haploview 4.0 program that we can download that program from
http://www.broad.mit.edu/mpg/haploview/download.php But this program must required
java program to manage with this program
1. Download Haploview 4.0 from
http://www.broad.mit.edu/mpg/haploview/download.php
2. Click download from Haploview menu
3.If your computer is window program click HapInstall.exe
4.Click save file
5. Click run
6. Click next
7.Click next
8.Click next
9.Click Finish and program will install on your computer.
10. pepare data that used in Data of Hapmap format.
- Copy data and open in Microsoft Word
- Save data in form Plain text
11. When open Haploview program we will found Welcome to HaploView- The picture show the window when we open Haploview program
- In Welcome to HaploView window select HapMap Download
Set up
- Release 21
- Select Chromosome that we want to study that in this study is Chromosome X
- Select population group that we want to study in this study select CHB+JPT. And then click OK to start work
- Click HapMap Format for download File and click OK
- Change HW p-value cut off to 0.05 and click Rescore Markers
- And then click Haplotypes the result show as picture
- Show result window in LD Plot
How many haplotype blocks in this region of Chromosome X?
In LD plot the result show
from the result have 3 haplotype blocks are
- Block 1 position 8, 9
- Block 2 position 13, 14, 15, 16, 17
- Block 3 position 24, 25, 26, 27, 28, 29
V. Could you find out the tagging SNP in each haplotype block?
After recieve the result from window Haplotypes for present tagging SNP in each
haplotype block select Display click ''Show tags in blocks'' will present as picture
present Haplotype block window that present tagging SNP
•Result present tagging SNP are
Block 1 have tagging SNP in position 8,9
Block 2 have tagging SNP in position 13,15
Block 3 have tagging SNP in position 24,27
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