Table 1.
List of SNPs tested for LD with the BTNL8*3 deletion CNV
| |
|
|
ASW |
|
CEU |
|
CHB |
|
CHD |
|
GHI |
|
JPT |
|
LWK |
|
MKK |
|
MEX |
|
TSI |
|
YRI |
|
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| rs Number | Position | Distance to deletion breakpoints | D' | r2 | D' | r2 | D' | r2 | D' | r2 | D' | r2 | D' | r2 | D' | r2 | D' | r2 | D' | r2 | D' | r2 | D' | r2 |
| rs1904435 |
180322735 |
52,292 |
|
|
|
|
0.94 |
0.834 |
1 |
0.77 |
0.81 |
0.596 |
1 |
0.829 |
0.31 |
0.03 |
|
|
0.93 |
0.537 |
0.8 |
0.495 |
0.69 |
0.099 |
| rs7735361 |
180329359 |
45,668 |
1 |
0.086 |
0.91 |
0.843 |
1 |
0.658 |
1 |
0.706 |
0.94 |
0.663 |
1 |
0.796 |
0.3 |
0.034 |
0.37 |
0 |
0.82 |
0.58 |
0.8 |
0.54 |
0.03 |
0 |
| rs17704291 |
180336849 |
38,178 |
0.8 |
0.43 |
1 |
0.96 |
0.94 |
0.889 |
- |
- |
- |
- |
1 |
1 |
0.28 |
0.04 |
|
|
0.94 |
0.76 |
0.9 |
0.68 |
0.3 |
0.06 |
| rs4700772 |
180341845 |
33,182 |
0.8 |
0.539 |
1 |
1 |
1 |
1 |
1 |
0.966 |
1 |
0.946 |
1 |
1 |
0.8 |
0.25 |
0.63 |
0.322 |
1 |
0.952 |
1 |
0.752 |
0.8 |
0.3 |
| rs2387715 |
180361266 |
13,761 |
0.8 |
0.694 |
1 |
1 |
1 |
1 |
1 |
0.966 |
1 |
0.944 |
1 |
1 |
0.8 |
0.237 |
0.63 |
0.322 |
1 |
0.952 |
1 |
0.749 |
0.8 |
0.33 |
| rs3733755 |
180374484 |
543 |
1 |
0.686 |
1 |
0.815 |
1 |
0.692 |
1 |
0.451 |
1 |
0.588 |
1 |
0.486 |
1 |
0.31 |
0.77 |
0.195 |
1 |
0.86 |
1 |
0.598 |
1 |
0.38 |
| deletion |
180375027-180430596 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| rs10063135 |
180432024 |
1,428 |
1 |
0.177 |
1 |
0.923 |
1 |
0.946 |
1 |
0.966 |
1 |
0.545 |
1 |
0.754 |
0.4 |
0.161 |
0.8 |
0.101 |
1 |
0.82 |
0.97 |
0.81 |
0.8 |
0.09 |
| rs4700774 |
180434216 |
3,620 |
1 |
0.473 |
1 |
1 |
1 |
0.945 |
1 |
0.966 |
1 |
0.893 |
1 |
1 |
0.84 |
0.12 |
0.5 |
0.09 |
0.95 |
0.903 |
1 |
0.752 |
0.2 |
0.07 |
| rs7721042 |
180439488 |
8,892 |
|
|
1 |
0.958 |
1 |
0.939 |
- |
- |
- |
- |
1 |
1 |
- |
- |
|
|
|
|
- |
- |
0.03 |
0 |
| rs11249756 |
180455372 |
24,776 |
1 |
0.473 |
1 |
0.923 |
1 |
0.945 |
0.96 |
0.86 |
0.8 |
0.64 |
1 |
1 |
0.4 |
0.161 |
0.44 |
0.07 |
0.94 |
0.807 |
0.94 |
0.72 |
0.2 |
0.07 |
| rs4701016 |
180458539 |
27,943 |
1 |
0.686 |
0.91 |
0.733 |
1 |
0.646 |
0.86 |
0.37 |
0.6 |
0.3 |
1 |
0.486 |
1 |
0.364 |
0.2 |
0.01 |
0.85 |
0.719 |
0.9 |
0.55 |
1 |
0.3 |
| rs6868418 | 180458813 | 28,217 | 1 | 0.686 | 0.91 | 0.733 | 1 | 0.646 | 0.86 | 0.4 | 0.6 | 0.3 | 1 | 0.486 | 1 | 0.364 | - | - | - | - | - | - | 1 | 0.3 |
HapMap phase III populations were screened for tagging SNPs for the BTNL8_BTNL3-del allele. Several SNPs could be identified in Eastern Asian (CHB, CHD and JPT), American (GIH and MEX) and CEU population. However, no LD could be observed in African population (ASW, LKW, MKK and YRI) and only a weak association for rs10063135 could be detected in TSI population.
r2 higher than0.8 indicates a significant correlation. ASW, individuals with African ancestry from Southwest USA; CEU, individuals from Utah with northern and western European ancestry; CHB, Han Chinese from Bejing; CHD, Han Chinese from Denver, Colorado; GIH, Gujarati Indians from Houston, Texas; JPT, Japanese from Tokyo; LWK, Luhya from Webuya, Kenya; MEK, individuals with Mexican ancestry from Los Angeles, California; MKK, Maasai from Kinyawa, Kenya; TSI, Toscans from Italy; YRI, Yorubas from Ibadan, Nigeria.