SNP arrays

A method for identifying a functional single nucleotide polymorphism (SNP) that modulates binding of a protein to a nucleic acid comprising said functional SNP, said method comprising:

• a) providing a microarray comprising a plurality of probes on a substrate, wherein each probe is a hairpin or double-stranded nucleic acid having a nucleotide sequence comprising a test allele of a SNP and wherein said plurality of probes comprises a probe comprising an allele of rs10453084, a probe comprising an allele of rs10825652, a probe comprising an allele of rs2047025, a probe comprising an allele of rs2660766, a probe comprising an allele of rs4242403, a probe comprising an allele of rs9910829, and a probe comprising an allele of rs62062347;
• b) contacting the microarray with a protein;
• c) measuring a first binding affinity and/or specificity of the protein for a probe having a nucleotide sequence comprising a test allele of a SNP, wherein said first binding affinity and/or specificity is different than a second binding affinity and/or specificity of said protein for a probe having a nucleotide sequence comprising an alternative allele of said SNP;
• and
• d) identifying said SNP detected to have different first and second binding affinities and/or specificities for the protein to be a functional SNP that modulates binding of said protein to a nucleic acid comprising said functional SNP.