SNP Proxies
I made a simple web service to list proxies for SNPs in the 1000 Genomes Project. Check out an example of the JSON output. I used it to make an application powered by Highcharts for viewing the r2 linkage disequilibrium plot of any SNP in any population.
Application
Details
For each SNP, I precomputed the r2 and D’ values for all neighboring SNPs within a 1 Mb window. I did this for each population (AFR, AMR, ASN, EUR). Next, I wrote a PHP script to retrieve those precomputed values from my files.
You can download the data files here:
http://broadinstitute.org/~slowikow/tgp/pairwise_ld/
Contact me if you’d like the code for computing these values.
Example
http://www.broadinstitute.org/~slowikow/snp_proxies.php?q=rs42&r2=0.95&pop=ASN
Parameters
Name Example Description
---- ------- -----------
q q=rs42 rs identifier of a SNP.
pop pop=EUR 1000 Genomes population used to compute r2 and D'.
r2 r2=0.5 Pearson correlation coefficient.
dp dp=0.5 D' value.
Output
{
"status": "found proxies",
"snp": {
"name": "rs42",
"chrom": "chr7",
"pos": 11586351
},
"r2": 0.95,
"dp": 0,
"pop": "ASN",
"proxies": [
{
"name": "rs55",
"chrom": "chr7",
"pos": 11585628,
"r2": 1,
"dp": 1
},
{
"name": "rs54",
"chrom": "chr7",
"pos": 11586050,
"r2": 0.991171,
"dp": 1
},
{
"name": "rs44",
"chrom": "chr7",
"pos": 11586190,
"r2": 0.991171,
"dp": 1
},
{
"name": "rs43",
"chrom": "chr7",
"pos": 11586267,
"r2": 0.991171,
"dp": 1
}
]
}