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Table 1 Some clear, consistent common disease associations.

From: Functional single nucleotide polymorphism-based association studies

Gene Disease Presumed
causative
variant
Functional effect Approximate frequency
(in ethnic population of
first positive study)
Frequency information
For other populationsa
PTPN22 Rheumatoid
arthritis [313]
R620W nsSNP 9-10% (Caucasian)[313] 0% in n = 1,600 Japanese;
0% in n = 60 Africans [3, 14]
- Type 1
diabetes [7, 9, 1520]
- - - -
CFH
(factorH)
Macular
degeneration [2126]
Y402H nsSNP 30 40%
(Caucasians)[2126]
Unknown
FV
(factor5)
Deep venous
thrombosis [2734]
R506W nsSNP 3 7% (Caucasians)[35] 0% in n = 800 from Africa,
South-East Asia, Australasia and the
Americas (Native) [35, 36]
F2
(prothrombin)
Deep venous
thrombosis [34, 3740]
G20210A 3' utr mRNA
cleavage site [41]
1 3% (Caucasians)[42] 0% in Asians;0% in Africans [36, 40, 42]
CARD15
(NOD2)
Crohn's
disease [4346]
1007fs Frame shift causing
truncated protein
~2% (Caucasians) 0% in [Q3] n = 888 Asians; 0% in n = 640 Gambians [4749]
- - R702W nsSNP ~4% (Caucasians) < 0.1% in 888 Asians; 0% in 640 Gambians [4749]
- - G908R nsSNP ~1% (Caucasians) < 0.1% in n = 888 Asians; 0% in n = 640 Gambians [4749]
- - Several very
rare variants
nsSNPs < 1% (Caucasians) Unknown
CHEK2 Breast cancer [5056] 1100delC Frame shift causing
truncated protein
0.5-1.5% (Caucasians)[5056] Unknown
APOE Alzheimer's
disease [5760]
C112R nsSNP ~15% (Caucasians)[5761] 25 40% in Africans; 8% in Asians [6265]
KCNJ11 Type 2 diabetes [66, 67] E23K nsSNP ~40% (Caucasians)[68] Unknown
CCR5 HIV infection [6973] Delta32 Frame shift causing truncated protein 8 10% (Caucasians)[6973] Absent in Africans and Asians; 2 5% in the Middle East, India, Europe [74]
HLA-
various genes
Many autoimmune
diseases
Varied Largely
nsSNPs/haplotypes
Varied Varied; many show striking population frequency differences
  1. Abbreviations: nsSNP = non-synonymous single nucleotide polymorphisms; utr = untranslated regions.
  2. a With the exception of HLA and APOE, none of the presumed causative variants have been shown to be present above 1 per cent in multiple major ethnic populations. While the 112R allele of APOE (which defines APOE*4 from the major allele, APOE*3) is seen in African, Asians and Caucasians, this variant is not associated with Alzheimer's disease in African populations [63].