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Resources at HapMap.Org. Tutorial Marcela K. Tello-Ruiz Cold Spring Harbor Laboratory. HapMap Phase II Dataset . Release #21a, January 2007 (NCBI build 35) 3.8 M genotyped SNPs => 1 SNP/700 bp. # polymorphic SNPs/kb in consensus dataset.

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resources at hapmap org

Resources at HapMap.Org


Marcela K. Tello-Ruiz

Cold Spring Harbor Laboratory

hapmap phase ii dataset
HapMap Phase II Dataset

Release #21a, January 2007 (NCBI build 35)

3.8 M genotyped SNPs => 1 SNP/700 bp

# polymorphic SNPs/kb in consensus dataset

International HapMap Consortium (2007). Nature 449:851-861

goals of this tutorial
Goals of This Tutorial

This tutorial will show you how to:

  • Find HapMap SNPs near a gene or region of interest (ROI)
    • View patterns of LD in the ROI
    • Select tag SNPs in the ROI
    • Download information on the SNPs in ROI for use in Haploview
    • Add custom tracks of association data
    • Create publication-quality images
  • Generate customized extracts of the entire data set
  • Download the entire data set in bulk
finding hapmap snps in a region of interest
Finding HapMap SNPs in a Region of Interest
  • Find the TCF7L2 gene
  • Identify the characterized SNPs in the region
  • View the patterns of LD (NCBI b35)
  • Pick tag SNPs (NCBI b35)
  • Download the region in Haploview format
  • Upload your own annotations & superimpose on the HapMap
  • Make a customized image for publication
  • View GWA hits & OMIM annotations in the region (NCBI b36)
hapmap glossary
HapMap Glossary
  • LD (linkage disequilibrium):For a pair of SNP alleles, it’s a measure of deviation from random association (which assumes 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 SNPs are redundant, so either one “tags” the other.
  • Questions?
1 surf to the hapmap browser
1: Surf to the HapMap Browser

1a. Go to

1b. Select “HapMap Genome Browser B35”

ncbi B35: full dataset (includes LD patterns)

ncbi B36: latest, new tracks (e.g., GWA hits)

2 search for tcf7l2
2: Search for TCF7L2

Search for a gene name, a chromosome band, or a phrase like “insulin receptor”

2. Type search term – “TCF7L2”

3 examine region

Chromosome-wide summary data is shown in overview

3: Examine Region

Region view puts your ROI in genomic context

3: This exonic region has many typed SNPs. Click on ruler to re-center image.

Default tracks show HapMap genotyped SNPs, refGenes with exon/intron splicing patterns, etc.

3 examine region cont
3: Examine Region (cont)

Use the Scroll/Zoom buttons and menu to change position & magnification

As you zoom in further, the display changes to include more detail

4 turn on ld haplotype tracks
4: Turn on LD & Haplotype Tracks

4a: Scroll down to the “Tracks” section. Turn on the LD Plot and Haplotype Display tracks.

4b: Press “Update Image”

These sections allow you to adjust the display and to superimpose your own data on the HapMap

5 view variation patterns
5: View variation patterns

Triangle plot shows LD values using r2 or D’/LOD scores in one or more HapMap population

Phased haplotype track shows all 120 chromosomes with alleles colored yellow and blue

7 adjust track settings on the spot
7: Adjust Track Settings (on the spot)

7a. Click on question mark preceding

track name

7b. Adjust population and display settings & press “Configure”

7 adjust track settings cont
7: Adjust Track Settings (cont)

Select the analysis track to adjust and press “Configure”

8 turn on tag snp track
8: Turn on Tag SNP Track

8: Activate the “tag SNP Picker” and press “Update Image”

9 adjust tag snp picker
9: 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…”

9a: Click on question mark behind “tag SNP Picker”

9 adjust tag snp picker cont
9: Adjust tag SNP picker (cont)

Select population

Select tagging algorithm and parameters

[optional] upload list of SNPs to be included, excluded, or design scores

9b: Press “Configure” to save changes

10 generate reports
10: Generate Reports

10: Select the desired “Download” option and press “Go” or “Configure”

  • Available Downloads:
  • Individual Genotypes
  • Population Allele & Genotype frequencies
  • Pairwise LD values
  • Tag SNPs
10 generate reports cont
10: Generate Reports (cont)

The Genotype download format can be saved to disk or loaded directly into Haploview

10 generate reports cont1
10: Generate Reports (cont)

The tag SNP download is the same as you get from TAGGER

11 create your own tracks
11: Create your own tracks


  • Interested in T2DM genetics
  • Create file with custom annotations from and superimpose on the HapMap

11: Upload example file: TCF7L2_annotations.txt

Detailed help on the format is under the “Help” link

11 create your own tracks cont
11: Create your own tracks (cont)

Formatted data for the T2DM association results (score is

-LOG10 of p-value)

Some SNPs were typed (known platform) and others were imputed. Format data for both typed & imputed SNPs.

Save as a text file!

11 create your own tracks cont2
11: Create your own tracks (cont)

Make edits on your own browser window by clicking on “Edit File…”

12 create image for publication
12: Create Image for Publication

Click on the +/- sign to hide/show a section

12a. Click on “High-res Image”

Mouse over a track until a cross appears.

Click on track name to drag track up or down.

12 image for publication cont
12: Image for Publication (cont)

12b. Click on “View SVG Image in new browser window”

12c. Save generate 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

12 image for publication cont1
12: Image for Publication (cont)

Inskape is free and lets you edit and convert to other formats (many journals prefer EPS)

13 view gwa hits
13: View GWA hits

13a. Go to

13b. Select “HapMap Genome Browser B36”

13 view gwa hits cont
13: View GWA hits (cont)

13c. Type search term - “FTO”

Default tracks for B36 include GWA hits, OMIM predicted associations, and Reactome pathways

14 read pubmed abstracts for gwa hits
14: Read PubMed abstracts for GWA hits

14a: Mouse over a GWA hit to learn more about the association

14b: Click on the GWA hit to see the study’s PubMed abstract

use hapmart to generate extracts of the hapmap dataset
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
1 go to hapmart hapmap org
1. Go to

1. From click on “HapMart”

2 select data source and population of interest
2. Select data source and population of interest

2b. Press “Next”

Use schema menu to select dataset

2a. Choose Yoruba population or “All Populations”

3 select the desired filters
3. Select the desired filters

3c. Press “Next”

3a. Check “Allele Frequency Filter” and select MAF >= 0.2

3b. Select “SNPs found in Exons – non synonymous coding SNPs”

4 select output fields
4. Select output fields

4c. Press “Export”

The summary shows active filters and # SNPs to be output

4a. Choose among several pages of fields

Options at the bottom let you select text or Excel format

4b. Select the fields to include in the report.

bulk downloads download the complete data
Bulk downloads: Download the Complete Data
  • Download the entire HapMap data set to your own computer
surf to www hapmap org
Surf to

Or directly click on “Data”

1. From, click on “Bulk Data Download”

2 choose the data type
2. Choose the Data Type

2. Select “Genotypes”

Raw genotypes & frequencies

Analytic results

Protocols & assay design

Your own copy of the HapMap Browser

HapMap Samples

* Data also available via FTP

3 choose the dataset of interest
3. Choose the dataset of interest

3. Select latest build, fwd_strand orientation, and “non-redundant”

fwd_strand => same as NCBI reference assembly

rs_strand => same as in dbSNP

  • Available Genotype Datasets:
  • Non-redundant: QC+ filtered & redundant data removed
  • Filtered-redundant: QC+ filtered; duplicated data not removed
  • Unfiltered-redundant: Includes assays that failed QC
further information
Further Information
  • HapMap Publications & Guidelines

  • Past tutorials & user’s guide to

  • Questions?

HapMap DCC Present Members (CSHL)

Lincoln Stein

Marcela K. Tello-Ruiz

Lalitha Krishnan

Zhenyuan Lu

HapMap DCC Former Members

Albert Vernon Smith

Gudmundur Thorisson

Fiona Cunningham