1. Resources at HapMap.Org
HapMap3 Tutorial
Marcela K. Tello-Ruiz
Cold Spring Harbor Laboratory

2. Low LD -> Recombination
Basic Concepts
Parent 1
Parent 2
A B
a b
A B
a b X
A B
a b
A b
A B
A B
a b OR
a B
A B
A b
a b
A B
a B
A b
A B
a b
A B
etc…
High LD -> No Recombination
(r2 = 1) SNP1 “tags” SNP2
Low LD -> Recombination
Many possibilities

3. Basic Concepts SNP1 SNP2 alleles: A/a B/b C1 C2
POP allele freqs: A (80%) B (60%)
a (20%) b (40%)
genotypes:
Person 1 Person 2 Person 3
AA AA Aa
BB Bb Bb
phased haplotypes (C1/C2):
A B A B A B A B A b a b OR
A b
a B

4. HapMap Glossary
LD (linkage disequilibrium): For a pair of SNP alleles, it’s a measure of deviation from random association (i.e., no recombination). Measured by D’, r2, LOD
Phased haplotypes: Estimated distribution of SNP alleles. Alleles transmitted from Mom are in same chromosome haplotype, while Dad’s form the paternal haplotype.
Tag SNPs: Minimum SNP set to identify a haplotype. r2= 1 indicates two SNPs are redundant, so each one perfectly “tags” the other.
Questions?

5. HapMap International Consortium
HapMap Project
Phase 1
Phase 2
Phase 3
Samples & POP panels
269 samples
(4 panels)
270 samples
1,115 samples
(11 panels)
Genotyping centers
HapMap International Consortium
Perlegen
Broad & Sanger
Unique QC+ SNPs
1.1 M
3.8 M
(phase I+II)
1.6 M (Affy 6.0 & Illumina 1M)
Reference
Nature (2005) 437:p1299
Nature (2007) 449:p851
Draft Rel. 1
(May 2008)

6. 3.9 M unique QC+ SNPs -- > 1 SNP/700 bp
Release Notes
Phase 1+2: Latest Release #24, October 2008 (NCBI build 36):
3.9 M unique QC+ SNPs -- > 1 SNP/700 bp
Added back chrX SNPs dropped in previous releases
Corrected allele flips from rel#23a
Phase 3: Draft release #1 (NCBI build 36)
HapMap3 Broad Institute, Sanger Center and Baylor College

7. Phase 3 Samples
* Population is made of family trios

8. Phase 3 11 panels & 1,115 samples Platforms:
558/557 males/females
924/191 founders/non-founders
Platforms:
Illumina Human 1M (Sanger)
Affymetrix SNP 6.0 (Broad)
EXCLUDED from QC+ data set:
Samples with low completeness, and SNPs with low call rate in each pop (< 80%) and not in HWE (p < 0.001)
Overall false positive rate: ~3.2%
Data merged with PLINK (concordance over 249,889 overlapping SNPs = )
Alleles on the (+/fwd) strand of NCBI b36

9. Phase 3: Draft Release 1 samples QC+ SNPs poly QC+ SNPs 71 ASW
1,632,186
1,536,247
162 CEU
1,634,020
1,403,896
82 CHB
1,637,672
1,311,113
70 CHD
1,619,203
1,270,600
83 GIH
1,631,060
1,391,578
82 JPT
1,637,610
1,272,736
83 LWK
1,631,688
1,507,520
71 MEX
1,614,892
1,430,334
171 MKK
1,621,427
1,525,239
77 TSI
1,629,957
1,393,925
163 YRI
1,634,666
1,484,416

10. Phase 3 Data HapMap format:
* Excluded 1,527 SNPs with strandedness issues & 411 indels
PLINK format:
HapMap3 sites:
Broad -
Sanger -
Baylor -

11. Goals of This Tutorial This tutorial will show you how to:
Find HapMap3 SNPs near a gene or region of interest (ROI)
Visualize allele frequencies in HapMap3 populations
Download SNP genotypes in ROI for use in Haploview 4.1
Identify GWA hits in the vicinity of ROI & visualize in the context of all chromosomes (karyogram)
Add custom data onto the GWAs karyogram
Add custom tracks of association data onto ROI
Create publication-quality images
Download the entire HapMap3 data set in bulk
Distinguish genotype data in PLINK and HapMap formats
Visualize LD patterns, find tag SNPs, impute genotypes using release #24 (phase 1+2)
Generate customized extracts of the entire dataset using HapMart

12. 1: Surf to the HapMap Browser
1a. Go to
1b. Select “HapMap phase 3”

13. 2. Type search term – “TCF7L2”
2: Search for TCF7L2
Search for a gene name, a chromosome band, or a phrase like “insulin receptor”
2. Type search term – “TCF7L2”

14. 3: Examine Region
Chromosome-wide summary data is shown in overview
Region view puts your ROI in genomic context
Default tracks show HapMap genotyped SNPs, refGenes with exon/intron splicing patterns, etc.
3: This exonic region has many typed SNPs. Click on ruler to re-center image.

15. 3: Examine Region (cont)
Use the Scroll/Zoom buttons and menu to change position & magnification
3: Mouse over a SNP to see allele frequency table
As you zoom in further, the display changes to include more detail
Click to go to SNP details page

16. 4: Generate Text Reports
4: Select the desired “Download” option and press “Go” or “Configure”
Available phase 3 downloads:
- Individual genotypes
- Population allele & genotype frequencies

17. 4: Generate Reports (cont)
The Genotype download format can be saved to disk or loaded directly into Haploview v4.1

18. 5b: Find GWA hits in nearby region. Click on a GWA hit to re-center
5a: Scroll down to turn on GWA studies tracks in overview & region panels
5b: Find GWA hits in nearby region. Click on a GWA hit to re-center

19. 5c: Mouse over & click on GWA hit for more info
5: Find GWA hits (cont)
5c: Mouse over & click on GWA hit for more info

20. 6: Examine GWA hits in entire genome
6: From select “Karyogram”

21. 6: Custom GWA hits in karyogram
6: Follow these instructions to upload your own GWA data
Detailed help on the format is under the “Help” link

22. 7: Create your own tracks
Example:
Interested in T2DM genetics
Create file with custom annotations from and superimpose on the HapMap
7: Upload example file: TCF7L2_annotations.txt
Detailed help on the format is under the “Help” link

23. 7: Create your own tracks (cont)
Some SNPs were typed (known platform) and others were imputed. Format data for both typed & imputed SNPs.
Scores allow you to display data in quantitative form, such as XY plots
Save as a text file!

24. 7: Create your own tracks (cont)
Remember to point your browser to the location of your annotations (TCF7L2 gene in this case).

25. 7: Create your own tracks (cont)
Make edits on your own browser window by clicking on “Edit File…”

26. 7: Create your own tracks (cont)

27. 8: Create Image for Publication
Click on the +/- sign to hide/show a section
8a. Click on “High-res Image”
Mouse over a track until a cross appears.
Click on track name to drag track up or down.

28. 8: Image for Publication (cont)
8b. Click on “View SVG Image in new browser window”
8c. Save generated file with “.svg” extensions
Can view file in Firefox, but use other programs (Adobe Illustrator or Inkscape) to convert to other formats and/or edit

29. 8: Image for Publication (cont)
Inkscape is free and lets you edit and convert to other formats (many journals prefer EPS)

30. 9. Bulk downloads
Or directly click on “Data”
18. From click on “Bulk Data Download”

31. HapMap3 genotypes & frequencies
9. Bulk downloads
Download the entire HapMap3 data set to your own computer
HapMap3 genotypes & frequencies
9a. Select “Genotypes”
Analytic results (LD & phased haplotype data available for HapMap3)
Your own copy of the HapMap Browser
Protocols & assay design
HapMap Samples
Also available at

32. 9b. Click on hapmap_format/forward to download genotypes
9. Bulk downloads (cont)
9b. Click on hapmap_format/forward to download genotypes
Also at

33. 10: Surf to the HapMap phase 1+2 genome browser
10. Go to & select “HapMap Genome Browser B36”

34. 11. Type search term – “TCF7L2”
11: Search for TCF7L2
11. Type search term – “TCF7L2”

35. 12: Examine Region
12. Re-center & zoom in

36. 12: Turn on LD & Haplotype Tracks
12a: Scroll down to the “Tracks” section. Turn on the LD Plot and Haplotype Display tracks.
12b: Press “Update Image”
These sections allow you to adjust the display and to superimpose your own data on the HapMap

37. 13: View variation patterns
Triangle plot shows LD values using r2 or D’/LOD scores in one or more HapMap populations
Phased haplotype track shows all 120 chromosomes with alleles colored yellow and blue

38. 14: Adjust Track Settings (on the spot)
14a. Click on question mark preceding
track name
14b. Adjust population and display settings & press “Configure”

39. 14: Adjust Track Settings (cont)
Select the analysis track to adjust and press “Configure”

40. 15: Activate the “tag SNP Picker” and press “Update Image”
15: Turn on Tag SNP Track
15: Activate the “tag SNP Picker” and press “Update Image”

41. 16: Adjust tag SNP picker
Tag SNPs are selected on the fly as you navigate around the genome
Alternatively, you may select “Annotate tag SNP Picker” and press “Configure…”
16a: Click on question mark behind “tag SNP Picker”

42. 16: Adjust tag SNP picker (cont)
Select population
Select tagging algorithm and parameters
[optional] upload list of SNPs to be included, excluded, or design scores
16b: Press “Configure” to save changes

43. 17: Impute genotypes using HapMap Data
Interested in the VAV1 gene
Commercially available platforms with few overlapping SNPs in this region
HapMap genotyped lots of SNPs in region
Use genotypes for HapMap SNPs to impute genotypes & compare non-overlapping SNP sets!

44. 17: Impute genotypes using MACH1
17b. Select “Download Impute Data”, click “Configure”
17a. Go to chr19:6,765,000..6,900,000

45. 17: Configure MACH1
17c. Upload input files: example.dat & example.ped. Enter address. Click “Go”

46. 17: Impute genotypes: Input files
example.dat (20 user-provided SNPs; all should be part of the HapMap):
M rs
M rs164022
M rs625828
M rs461970
M rs331684 …
example.ped (genotypes for 336 unrelated inds):
PED IND C/C C/C T/T C/T C/C G/G G/G …
PED IND C/T C/C T/T T/T C/C A/A A/G …
PED IND T/T G/G A/A C/T C/C A/G A/G …

47. 17. Visualize imputed SNPs
17d. Return to browser
17. Visualize imputed SNPs
Your imputation results appear as an external track that can be edited.
Hint: Click on “Help” link below for display options
17e. Click “Edit File”

48. 17. Edit external annotations file
17f. Edit annotations file & “Submit Changes”

49. 17. Edit external annotations file

50. 17: Impute genotypes: Results
17g. Check your for text results
Info (143 provided & imputed HapMap SNPs)
SNP Al1 Al2 Freq1 MAF Quality Rsq
rs T A
rs T A
rs A G
rs T C
rs T C …
Geno (143 SNPs x 336 inds)
PED00001->IND00001 ML_GENO T/T T/T G/G C/C T/T T/T A/T G/G A/A T/T T/C …
PED00002->IND00002 ML_GENO T/T T/T A/G T/C T/T T/T A/T G/G A/A T/T T/C …
PED00003->IND00003 ML_GENO T/T T/T A/A T/T T/T T/T A/T G/G A/A T/T T/T …
Dose (allele dosage)
PED00001->IND00001 ML_DOSE …
PED00002->IND00002 ML_DOSE …
PED00003->IND00003 ML_DOSE …
Probability of match imputed:experimental genotype (1.0 for provided markers)

51. 18. Use HapMart to Generate Extracts of the HapMap Dataset
Find all HapMap characterized SNPs that:
Have a MAF > 0.20 in the Yoruban population panel (YRI)
Cause a nonsynonymous amino acid change
Were typed by Perlegen

52. Further Information HapMap Publications & Guidelines
Past tutorials & user’s guide to HapMap.org
Questions?

53. HapMap DCC Present Members (CSHL)
Lincoln Stein
Marcela K. Tello-Ruiz
Zhenyuan Lu
Wei Zhao
HapMap DCC Former Members
Lalitha Krishnan
Albert Vernon Smith
Gudmundur Thorisson
Fiona Cunningham