Neanderthal DNA linked disease?

I only have a link to a summary, but this article claims that Neanderthal DNA is associated with a lot of diseases.

NASHVILLE, TENNESSEE—Researchers from Vanderbilt University used a database of 28,000 anonymous individuals, whose DNA samples were linked to their electronic health records, to look for Neanderthal DNA variants and see if they could be connected to modern health problems. “Our main finding is that Neanderthal DNA does influence clinical traits in modern humans: We discovered associations between Neanderthal DNA and a wide range of traits, including immunological, dermatological, neurological, psychiatric, and reproductive diseases,” evolutionary geneticist John Capra said in a press release

Problem number one:

Association does not mean causation.
It could be coincidence. And unless one proves the Neanderthal DNA was in the part of the genome that was associated with the disease, the question of coincidence is likely.
one example can be found in the newspaper article stating that Neanderthals were redheads, so that would explain why some Europeans had red hair. A closer examination showed that the genes were different.

Problem two: Neanderthal DNA varies by race.

it is higher in East Asians than Europeans, but is almost non existent in Africans

didn't Vanderbilt have DNA from African Americans?
Depression and addiction and autoimmune disease are present in African Americans too.

But then I see: "Actinic keratoses" (pre skin cancer lesions). Uh, this merely means someone is pale and goes out in the sun a lot. Again a racial trait due to melatonin (and yes, African albinos get skin cancer too). So do neanderthal genes increase the risk, or is it higher in whites, and white Europeans have more Neanderthal genes? (skin color seems to be paler in northern climates, e.g. Korea...think VitaminD deficiency and ricketts..the exception is those who eat fatty fish like salmon...e.g. Eskimos...think cod liver oil).

The immune problem seems to be identified with the location of the gene in other studies, but the rest of these sound like junk science.

UKMail article. suggests the "interbreeding" stuff might be more complicated than earlier articles suggest.

but what is not clear when they say "x percent" of humans have neanderthal genes, if they mean X percent of the population, or if 100 percent of folks have x percent of the Neanderthal dna.

from Natgeo

Everyone living outside of Africa today has a small amount of Neanderthal in them, carried as a living relic of these ancient encounters. A team of scientists comparing the full genomes of the two species concluded that most Europeans and Asians have between 1 to 4 percent Neanderthal DNA. Indigenous sub-Saharan Africans have no Neanderthal DNA because their ancestors did not migrate through Eurasia.

so back to the original article: Did they actually check out the gene or not?

 For example, a Neanderthal variant that increases blood coagulation may have sealed wounds more quickly and prevented infections. 

John Hawks article on DNA in populations.
Wonder what the percentages would show for Mongolians/Koreans/Native Americans, who were from Siberia, not Han Chinese.

guess I'll have to do a bit more study into this area, because right now I'm confused at what is being claimed.