I know to use layers, and i do. 
But i don’t know it’s possible to say tile x is getting a transparency to only a color. 
I try the transparency (1,0…0,10) in tile properties but this make the tile transparent not only a color!
And if i import a tileset and set the transparent color it doesn’t work too! because the tiles color is not transparent. 
It should look like this:
But mine looks so:
The original tile:
so what are you trying to do ? 
didn’t get it
To get the result like the first picture shows!
The sand from the background should shine through the tile.
yeah so the first picture is confusing me a bit 
If you want a particular colour to be transparent, you’ll need to modify the image to make that colour transparent.
The “transparent color” feature for the tileset image is not generally meant to be used to add transparency to a tile. It is rather an alternative to using a full alpha layer, commonly used for 8-bit images (where each pixel refers to a color from a palette with up to 256 colors). One of the colors used in the palette (often “magic pink”, but not always hence it can be customized) is then not rendered at all.
But it seems you’re after partial transparency, where the background is blended with the foreground. If this should apply to a full tile layer, you can reduce the opacity of the layer. If it should only apply to some tiles, you’ll need to edit them in an image editor to reduce their opacity.