• Proxy Search
• Pairwise LD
• Plots
• Map SNP IDs
• ReACH

Enter a list of query snps or select a genomic locus to find pairs of input snps that meet the specified linkage disequilibrium threshold and other criteria.

Pair-wise linkage disequilibrium is pre-calculated based on phased genotype data from the International HapMap Project. Information about the genotyping arrays is based on data published by the vendors.

Query SNPs

Input SNPs: File Text Entry Genomic Locus (Limit 1Mb) Example

File:

SNP column:

Header line: yes no

One snp per line:

Chromosome: chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Start: End:

Search Options

SNP data set: HapMap release 21 HapMap release 22 HapMap 3 (release 2) 1000 Genomes Pilot 1

Population panel: CEU YRI JPT+CHB

r² threshold: 1.0 0.9 0.8 0.7 0.6 0.5 0.4 0.3 0.2 0.1 No limit

Distance limit: 0 10 25 50 100 250 500

Output Options

Download to: File Browser

Include each query snp as a proxy for itself

Suppress warning messages in output

Filter By Array

Limit search results to only SNPs on the selected arrays (select all)

Select All Illumina

Illumina Human-1 (I1)

Illumina HumanHap240S (I2)

Illumina HumanHap300 (I3)

Illumina Human370CNV single (IC)

Illumina Human370CNV quad (ICQ)

Illumina HumanHap550 (I5)

Illumina HumanHap650 (I6)

Illumina HumanHap610 quad (I6Q)

Illumina Human1M single (IM)

Illumina Human1M dual (IMD)

Illumina CARe iSelect (IBC)

Illumina Cyto12 (CYT)

Illumina OmniQuad (OQ)

Cardio-Metabochip (CM)

Illumina 660W-Quad (IWQ)

Illumina OmniExpress (OE)

Human Exome 12v1 (E1)

Human Exome 12v1.1 (E11)

OmniChip 2.5M 4 sam (O24)

OmniChip 2.5M 8 sam (O28)

OmniChip 5M 4 sam (O54)

Omni 5 Exome (O5E)

Omni Express Exome (OEE)

Immuno BeadChip A (ICA)

Immuno BeadChip B (ICB)

Select All Affymetrix

Affymetrix 50K Mapping XbaI (AX)

Affymetrix 50K Mapping HindIII (AH)

Affymetrix 50K Human Gene Focused chip (AG)

Affymetrix 250K Mapping NspI (AN)

Affymetrix 250K Mapping StyI (AS)

Affymetrix 5.0 (A5)

Affymetrix 6.0 (A6)

Affymetrix Axiom GW_Hu_SNP (AxM)

Affymetrix DMET plus (AD)

Affymetrix 10K Mapping Array bld2 (A10)

Affymetrix Axiom Exome Plus Array (AAE)

Affymetrix Axiom GW Hu Origins 1 (AAH)

Apply array filter to: query snps and proxy snps proxy snps only

Output Columns

Optional columns to include in the search results

D' (D prime)

Genome Coordinates

Array Membership

Recombination Rate (cM/Mb)

Genetic Distance (cM)

Genetic Map Position (cM)

Associated Gene Annotations from GeneCruiser (decreases performance)

Include Minor Allele Frequency