## Description

This track displays the SNPs used in genotyping platforms.

## Affymetrix Genome-Wide Human SNP Array 6.0

The SNP Array 6.0 includes more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 probes for the detection of copy number variation. The SNPs include the 482,000 SNPs from the 5.0 Array (unbiased selection). In addition, 424,000 new SNPs were chosen in the following areas:

- Tag SNPs
- SNPs from chromosomes X and Y
- Mitochondrial SNPs
- New SNPs added to dbSNP
- SNPs in recombination hotspots

The copy number probes include 202,000 probes targeting 5,677 known CNV regions from the Toronto Database of Genomic Variants. The additional 744,000 probes are evenly spaced throughout the genome.

## Affymetrix Genome-Wide Human SNP Array 5.0

The SNP Array 5.0 is a single microarray featuring all single nucleotide polymorphisms (SNPs) from the original two-chip Mapping 500K Array Set, as well as 420,000 additional non-polymorphic probes that can measure other genetic differences, such as copy number variation.

## Affymetrix 500K (250K Nsp and 250K Sty)

This annotation displays the SNPs available for genotyping with the GeneChip Human Mapping 500K Array Set from Affymetrix. It is comprised of two arrays: Nsp and Sty, which contain approximately 262,000 and 238,000 SNPs, respectively.

## Illumina HumanHap650Y

This annotation displays the SNPs available for genotyping with Illumina's HumanHap650Y Genotyping BeadChip. The HumanHap650Y contains over 650,000 markers, extending the HumanHap550 by adding 100,000 additional Yoruba-specific tag SNPs. On average, there is 1 SNP every 5.3 kb, 6.2 kb and 5.4 kb across the genome in the CEU, CHB+JPT and YRI populations, respectively. The HumanHap650Y was derived from release 21 of the International HapMap Project.

## Illumina HumanHap550

This annotation displays the SNPs available for genotyping with Illumina's HumanHap550 Genotyping BeadChip. The HumanHap550 contains over 550,000 markers, the majority of which are tag SNPs derived from release 20 of the International HapMap Project. In addition, approximately 7800 non-synonymous SNPs, a higher density of tag SNPs in the MHC region, over 150 mitochondrial SNPs and over 4000 SNPs from regions with copy number polymorphism were included. In the CEU population, an r-squared threshold of 0.8 was used for common SNPs in genes, within 10 kb of genes or in evolutionarily conserved regions. For all other regions, an r-squared threshold of 0.7 was used. On average, there is 1 SNP every 5.5 kb, 6.5 kb and 6.2 kb across the genome in the CEU, CHB+JPT and YRI populations, respectively.

## Illumina HumanHap300

This annotation displays the SNPs available for genotyping with Illumina's HumanHap300 Genotyping BeadChip. The HumanHap300 contains over 317,000 tagSNP markers derived from Phase I of the International HapMap Project. In addition, approximately 7300 non-synonymous SNPs and a higher density of tag SNPs in the MHC region were included. On average, there is 1 SNP every 9 kb across the genome and median spacing is 5 kb.

## Illumina Human1M-Duo

This annotation displays the SNPs available for genotyping with Illumina's Human1M-Duo Genotyping BeadChip. The Human1M-Duo contains more than 1,100,000 tagSNP markers and a set of ~60,000 additional CNV-targeted markers. . The median spacing is 1.5 kb (mean - 2.4 kb).

## References

More information on the Affymetrix arrays is available at these sites:

- Genome-Wide Human SNP Array 6.0.
- Genome-Wide Human SNP Array 5.0.
- Mapping 500K Array Set.

More information on the Illumina arrays is available at these sites:

- HumanHap650Y Genotyping BeadChip.
- HumanHap550 Genotyping BeadChip.
- HumanHap300 Genotyping BeadChip.
- Human1M-Duo Genotyping BeadChip.

## Methods

Position, strand, and polymorphism data were obtained from Affymetrix and supplemented with links to corresponding dbSNP rsIDs based on a positional lookup into dbSNP. The Affy 6.0 Array is based on dbSNP build 127; the Affy 5.0 Array is based on dbSNP build 126. The Affy 500K Array is based on dbSNP build 125 and was translated from hg17 by UCSC using rsID lookup. In fewer than 2% of the cases, a dbSNP rsID was not present in dbSNP at the Affymetrix array position. Reference allele information was retrieved from the UCSC database based on dbSNP position and strand data.
Illumina data were supplied as rsIDs and position based on dbSNP build 126. Strand, polymorphism and reference allele information was retrieved from the UCSC database based on rsID and position. The Illumina arrays are comprised of probes for 4 of the possible single-base substitutions: A/C, A/G, C/T and G/T. A/T and C/G probes will be available in future arrays.
For Illumina Human1M-Duo, the position, strand, polymorphism and reference allele information was retrieved from the snp129 table of UCSC database if the marker ID can be found in dbSNP 129, otherwise the information is retrieved from the data provided by Illumina.

## Credits

Thanks to Venu Valmeekam from Affymetrix and Luana Galver from Illumina for providing these data.