Characterization of rs11190870.

<p>(A) A schematic representation of the most significantly associated SNP, rs11190870, and the surrounding genome region with the chromatin fragments obtained by the 3C assay. Cross-linked chromatin was digested with <i>Sau</i>3AI (vertical red lines). The green broken lines indicate primer positions. The blue lines indicate vertebrate conservation. The arrowheads indicate PCR primers. (B) Electrophoretic mobility shift assay of rs11190870 using 17-bp DIG-labeled probes for risk (T) and non-risk (C) alleles. Excess unlabeled probes were used as competitors. The arrow indicates that some nuclear factor(s) bound with higher affinity to the risk allele. (C) Physical interaction of rs11190870 and the nearby genomic region with the promoter region of <i>LBX1-FLJ41350</i> in the 3C assay (lane 1: rhabdomyosarcoma cells, lane 2: A172 cells, lane 3: HeLa cells). The arrow indicates specific PCR products of the expected sizes derived from the indicated primer sets in (A). (D) Transcriptional activity of the <i>LBX1-FLJ41350</i> promoter region. Luciferase activity of the promoter fragment (-917 to +153; direction of <i>LBX1</i> transcription) and its reverse fragment (direction of <i>FLJ41350</i> transcription) was measured in A172 cells. (E) The effect of the 590-bp conserved region containing rs11190870 on the <i>LBX1</i> promoter in HEK 293T cells. Higher activity was observed for the risk allele (T) construct than for the non-risk allele construct (C). Luciferase activity was normalized to the internal control and expressed as a ratio relative to the promoter-less construct (ctrl). The data in (D) and (E) represent the mean ± standard error of two independent experiments. *<i>p</i> < 0.05.