Links not clickable because of z-index

Actually z-index only works with position so I gave the position:relative; to your .down class.

See the mentioned below CSS & DEMO.

.box{
        position: absolute;
        top: 20px;
        background: yellow;
        width: 100px;
        height: 100px;
        z-index: 1;  
    }

    .down {
        background: none repeat scroll 0 0 green;
        height: 400px;
        overflow: hidden;
        position: relative;
        z-index: 2;
    }

DEMO