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GWAS Data and Blood Specimen Results

Specimen data from many of the WHI Core and Ancillary studies (AS) is available in the WHI Investigator's dataset, the WHI Database, on WHI AS site pages, and/or on dbGaP. The studies with data available to investigators with approved access in the WHI Investigators' dataset is on page 2 of the Specimen Assay Results. Descriptions of those assays can be found on our Specimen Results Descriptions page. Data from BAAs and ASs are generally made available 1 year after the end of the study funding period.  Specimen data from BAAs and ASs may be requested earlier by contacting the BAA or AS PI for permission to use it. Note that any of transfer of associated WHI covariate data would require WHI approval and a signed data use agreement for the use of the data. Questions about the BAA and AS data sets should be addressed with the BAA or AS PIs.

See the following sets and types of data available on specific sub-groups of WHI participants.

Baseline CVD Biomarkers

A subset of WHI participants have CVD biomarkers at baseline through a core set of WHI studies (additional participants have had CVD biomarkers measured through smaller ancillary studies, but those are not described here). It is important to note that CVD Biomarkers were measured at two different labs using different methods. ~5,600 participants had baseline CVD biomarkers (plasma: lipids, serum: glucose and insulin) measured at MRL/PPD as a subset of the WHI core analytes measured in studies W1 (6% CT subsample) and W2 (1% OS measurement Precision Study). ~24,500 participants had baseline CVD biomarkers (Laboratory Methods: serum: lipids, glucose, insulin, creatinine, and CRP) measured at UMMC in studies W54 (African Americans and Hispanics), W58 (European Americans in the HT), W66 (LLS eligibility pool expansion), and AS422 (Native Americans). W54 and W58 together are often referred to as the "CVD Biomarker Cohort", but W66 and AS422 also contribute to the baseline CVD biomarker resource. The WHI blood draws were scheduled to be fasting draws, but in some cases participants were not fasting. Fasting status is indicated in the WHI database. 

Baseline CVD Biomarkers - subset of WHI core analytes

Serum: glu​cose and insulin 

EDTA plasma: lipids

Creatinine and CRP were NOT measured


Baseline CVD Biomarkers​ ​ ​

Serum: glucose, insulin, lipids, creatinine and CRP



​Lab: University of Minnesota (UMMC)

W1: 6% CT subsampleW2: 1% OS Measurement Precision study​W54: African American and HispanicW58: European American HTW66: LLS eligibility pool expansion ​AS422: Native American
​N=~4,546​N=~1,082​N=~12,157​N=~10,306​N=~1,502​N=~594​Total ~N
​A. Original CVD Biomarker Cohort (selected to be a representative subsample of WHI, tested at UMMC)




B. All CVD biomarkers tested at UMMC






​C. Core analyte subcohort (tested at MRL/PPD)




​D. All (tested at MRL/PPD and/or UMMC)









  • Counts are of the participants selected for a study, not the number with specimen results. A small number of participants selected for a study may not have results for one or more assays due to insufficient sample or assay failure.
  • 2,642 participants overlap between options B and C.


GWAS Harmonization and Imputation Project

GWAS has been performed through many WHI ancillary studies with different platforms and different outcomes/exposures of interest, but GWAS data from about 30,000 WHI participants were imputed into 1,000 Genomes data. The harmonization/imputation effort involves 6 different GWAS studies, as described in the table below. 1000 Genomes Project reference panel (1092 samples; v2.20101123 for GECCO; v3.20101123 for Hip Fracture, SHARE, GARNET, WHIMS+ MOPMAP). The Harmonized and Imputed GWAS data is available at dbGaP (phs000746), but not all directly genotyped data has been submitted.

​Hip Fracture












​GWAS platform

​Illumina 550K and 610KAffymetrix 6.0​​Illumina HumanOmni1-Quad v1-0 B​HumanOmniExpressExome 8v1_B​Illumina 610 and Cytochip 370K​Affymetrix Gene Titan, Axiom Genome-Wide Human CEU I

​Study Design

​Hip fracture case-control​Cohort, minorities​Case-control (diabetes, myocardial infarction, stroke, VTE), from hormone therapy trials​Cohort, selected from hormone therapy trials​Colorectal case-control​Ventricular ectopy cases and controls selected within Centers, seasons, and visit years of cases


​Mostly whiteBlack and Hispanic​​Mostly White​WhiteWhite and Black​​White

​Total N after QC



Other large WHI genetic studies

Included in the WHI Investigators' Data is a file indicating which participants have genetic data on dbGaP (see the dbGaP Data Dictionary). Genetic and phenotypic data are routinely submitted to dbGaP. Please refer to the dbGaP website for detailed information on what WHI datasets are currently available, instructions on how to access and download data, searchable FAQs, and dbGaP contact information. For genetic data that are not yet available on dbGaP, or for very limited genetic datasets, data may be available from the WHI Clinical Coordinating Center (CCC) as detailed in our policy for accessing WHI genetic data.

​Study Name (ID)Study Population (synopsis)​​Assays​Status/Notes
​PAGE I (M6)

​Y1: N~31,000 OS/CT

Y2: N~20,420

Y3/4: N~12,560

​Y1: AIMS, SNPs 6, Metabochip

Y2: SNPs 384a and SNPs 384b

Y3/4: Metabochip

​Y1-Y2 available on dbGaP. Note: ~10% of the Y1 participants are not dbGaP eligible.

Y3/4 Metabochip and phenotype data on AA, Hispanics, Asians, and Native Americans was uploaded to dbGaP in 2014.

​PAGE II (AS349)​N~12,000 minorities​Exome chip with additional minority content
​WHISP (M24)

​N~2,230 for sequencing

N~8,900 for replication

​Exome sequencing

Exome chip for replication

​TOPMed (AS564/AS576)​N~11,000 VTE, stroke, and controls

​AS564: Whole genome sequencing

AS576: RNA sequencing (subset of ~1,350)

​Data will be available on dbGaP
​Oncochip (M18)​N~9,553 (breast cancer cases and controls)​Illumina Oncochip (600K SNPs)
​LLS eligibility pool expansion (W66)​N~1,502 Long Life Study participantsGWAS (Illumina Omni Express/Exome)​​Data will NOT be harmonized or imputed. It has been submitted to dbGaP and is expected to be available soon.


Overlap of Harmonized and Imputed GWAS and Baseline CVD Biomarkers at UMMC

A cohort of approximately 23,500 participants has both Harmonized and Imputed GWAS at dbGaP1 and baseline CVD Biomarkers at UMMC.2 See the table below. Note that the number of participants in MRC, LLS, and BMD cohorts are each a subset for the approximately 23,500 participants, and that participants in these three groups are not mutually exclusive (for example, a participant may be in 1, 2, or all 3 of the subsets).

​WHI Study Population​~N participants​~N in MRC3​~N in LLS4​~N in BMD5
​Hormone Trial (HT)​14,032​8,629​4,621​953
​Non-Hormone Trial and OS​9,468​6,049​3,102​1,094


1 - Only dbGaP eligible participants are included in GWAS projects. GWAS includes the data from the Harmonized and Imputed GWAS set (see above) and W66. W66 GWAS data is not imputed or harmonized, but has been submitted to dbGaP (phs001614.v1.p3).

2 - Baseline and CVD biomarkers from W54, W58, W66, and AS422 are included above, and include HDL, LDL, total cholesterol, triglycerides, glucose, insulin, CRP, and creatinine measured at UMMC.

3 - MRC = Medical Record Cohort, and includes HT participants and African Americans/Hispanics enrolled in the WHI Extension Study 2 (2010 - 2015) (ES2). In ES2, the WHI outcomes are adjudicated only for MRC participants while cancer outcomes are adjudicated for all participants.

4 - LLS = Long Life Study. Between 2012 and 2013, 7,875 MRC participants completed an LLS visit. CVD Biomarkers were done on baseline and LLS visit blood samples. Sample available includes serum, EDTA plasma, RBCs, extracted DNA, and extracted RNA. See the Long Life Study page for more information.

5 - BMD = Bone Mineral Density participants; see description of BMD subsample on listing on Subsample Definitions page. Urine samples were also collected on the BMD participants.


Test Results Available for the Long Life Study blood collection (W64)

Between 2012 and 2013, 7,875 MRC participants completed an LLS visit with a blood draw (~14-19 years post baseline). The LLS blood draw was scheduled to be a fasting draw, but in some cases participants were not fasting. Fasting status is indicated in the WHI database.

Test results available for the LLS blood draw include:

  • CVD Biomarkers in serum at UMMC: glucose, insulin, creatinine, CRP, lipids
  • Complete blood count (CBC) with 26 variables including WBC, RBC, hemoglobin, hematocrit, platelet count, WBC differential (automated), and numerous indices

Note that participants selected for LLS phase I and II recruitment all had samples sent for baseline CVD biomarkers and GWAS. When the eligibility pool needed to be expanded due to low enrollment (Phase III of recruitment), the LLS phase III eligible participants had baseline CVD biomarkers and/or GWAS measured (W66). 

See the Long Life Study page for more information.


Core WHI Study Analytes

Performed on the CT 6% subsample (W1) at baseline, Years 1, 3, and 6, and on the OS Measurement Precision Study participants (W2 - 1% of OS participants) at baseline and Month 3. The 20 core analytes include:


Limitations on Use of Specimen Data in Public Datasets

Summary data may be used for all participants. However, not all participant samples may be used in studies that plan to deposit genetic data into public datasets such as dbGaP or BioLINCC. All genetic studies funded by NIH are now required to deposit the GWAS data into dbGaP. Restrictions apply based on whether the participant signed the WHI Supplemental Use Consent Form - see table below. A participant who previously signed the Supplemental Use Consent and later declines to have her DNA used, will be moved to the Refused category. 

​Supplemental Use Consent form ​​ ​Post Individual Data on Public Website
​Non-Commercial UseCommercial Use​
​Participant Signed (72.7%)


​Participant did not respond (8.6%) or died before able to sign (7.2%)​Yes​No
​Participant refused to sign (11.4%)




Related Publications

Baseline blood analyses for the CT and OS have been published in the following documents.

Baseline monographs 

See also the blood analytes tables under Baseline summary tables.

Contact the WHI Help Desk at if you need assistance or have questions.