var myVariable;

protected override void RenderContents(HtmlTextWriter writer)
    {
        EnsureChildControls();
        base.RenderContents(writer);

writer.BeginRender();
        writer.RenderBeginTag(HtmlTextWriterTag.Script);
        writer.AddAttribute(HtmlTextWriterAttribute.Type, "text/javascript");

        writer.Write("myJavaScriptVar = (" + myC#Var + ")");
writer.RenderEndTag();

Document.InvokeScript("eval", new object[] { "my_var_name" });