A potential functional SNP in intron 1 (rs563649) was recently indicated in association with pain perception.20 The HapMap LD data indicate that although this SNP not part of the “INT1” haplogroup, it is in high LD with SNPs of haplogroup 3 that includes variants in the proximal 5′ region (block 3). Notably, this haplogroup is rare in European Americans, but frequent in the African sample. It is possible that this SNP is a marker of regulatory variant/s in the proximal 5′ region.
