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MetaboChip SNP details

The "MetaboChip" is a custom Illumina iSelect genotyping array designed to test, in a cost-effective manner, ~200,000 SNPs of interest for metabolic and atherosclerotic / cardiovascular disease traits. Content on the chip was selected on the basis of large scale meta-analysis of relevant traits (including up to 100,000 individuals) and of HapMap and 1000 Genomes Project SNP content.

The chip was designed by representatives of the CARDIoGRAM (coronary artery disease), DIAGRAM (type 2 diabetes), GIANT (height and weight), MAGIC (glycemic traits), Lipids (lipids), ICBP-GWAS (blood pressure), and QT-IGC (QT interval) GWAS meta-analysis consortia. It supports genotyping of SNPs selected according to five sets of criteria: (1) individual SNPs displaying evidence for association in GWA meta-analyses to relevant metabolic and cardiovascular endpoints, (2) detailed fine mapping of loci validated at genome-wide significance from these meta-analyses, (3) all SNPs associated at genome-wide significance with any human trait, (4) "wildcard SNPs" selected by each meta-analysis Consortium for Consortium-specific purposes, and (5) other useful content, including SNPs that tag common copy number polymorphisms, SNPs in the HLA region, SNPs marking the X and Y chromosomes and mtDNA, and SNPs selected for sample fingerprinting that are also present on major genome-wide array products from Illumina and Affymetrix.

For a more detailed description on the MetaboChip, please read the full summary document (PDF) released to the participating consortia. You can access the full list of the SNPs included in the Metabochip in VCF format (Refer to The official VCF specification for the format details. Peter Chines at NIH substantially helped compiling additional information together). The files are compressed with bgzip, and can also be decompressed by gzip or other gzip-compatible softwares. Additional tabix index is also provided for retrieving a subset of SNPs based on genomic coordinates. (See tabix documentation for details). Additional details and contact info is available within the VCF files. Also, you can download the boundary information of the fine mapping loci too.

List of MetaboChip SNPs (VCF format)

Remapped to NCBI build 36 MetaboChip.markers.ncbi36.20101203.vcf.gz MetaboChip.markers.ncbi36.20101203.vcf.gz.tbi
Remapped to NCBI build 37 MetaboChip.markers.ncbi37.20101203.vcf.gz MetaboChip.markers.ncbi37.20101203.vcf.gz.tbi

Boundary of Fine Mapping Loci

NCBI build 36 coordinate metabochip-fine-mapping-summary-public-r.xls


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