Table 2 |
||||||||
|
25 Most significant results for multivariable-adjusted subclinical atherosclerosis measures in multiple arterial territories by GEE (2a), FBAT (2b) and linkage (2c) analyses |
||||||||
|
2a. Most significant results for GEE analyses for multivariable-adjusted subclinical atherosclerosis measures |
||||||||
|
|
||||||||
|
GEE rank |
Phenotype |
SNP |
Chr |
Physical location |
GEE P-value |
FBAT P-value |
Gene position |
Gene symbol |
|
|
||||||||
|
1 |
Internal carotid artery IMT |
rs1376877 |
2 |
204,097,596 |
3.8 × 10-7 |
0.15 |
IN |
ABI2 |
|
3 |
Coronary artery calcification |
rs2390582 |
1 |
90,655,928 |
1.4 × 10-6 |
0.34 |
OUT |
|
|
4 |
Abdominal aortic calcification |
rs3849150 |
10 |
49,779,229 |
1.6 × 10-6 |
4.0 × 10-3 |
NEAR |
LRRC18 |
|
6 |
Ankle brachial index |
rs2896103 |
5 |
13,817,419 |
4.5 × 10-6 |
0.01 |
IN |
DNAH5 |
|
7 |
Coronary artery calcification |
rs10483853 |
14 |
72,826,052 |
6.1 × 10-6 |
1.7 × 10-3 |
IN |
NUMB |
|
8 |
Common carotid artery IMT |
rs1400544 |
1 |
186,593,061 |
6.2 × 10-6 |
4.7 × 10-4 |
OUT |
|
|
9 |
Ankle brachial index |
rs7715811 |
5 |
13,822,974 |
6.4 × 10-6 |
0.02 |
IN |
DNAH5 |
|
10 |
Coronary artery calcification |
rs10507130 |
12 |
100,256,422 |
6.7 × 10-6 |
1.6 × 10-3 |
IN |
DRIM |
|
11 |
Ankle brachial index |
rs1320267 |
4 |
127,290,897 |
6.9 × 10-6 |
0.03 |
OUT |
|
|
13 |
Ankle brachial index |
rs1350445 |
11 |
91,591,802 |
8.5 × 10-6 |
0.07 |
OUT |
|
|
14 |
Ankle brachial index |
rs1502050 |
5 |
13,832,743 |
8.7 × 10-6 |
0.02 |
IN |
DNAH5 |
|
15 |
Coronary artery calcification |
rs10519394 |
4 |
137,962,214 |
1.1 × 10-5 |
0.03 |
OUT |
|
|
16 |
Internal carotid artery IMT |
rs683366 |
18 |
52,370,975 |
1.2 × 10-5 |
0.01 |
NEAR |
TXNL1 |
|
19 |
Abdominal aortic calcification |
rs2850711 |
18 |
59,938,018 |
1.5 × 10-5 |
0.05 |
IN |
C18orf20 |
|
20 |
Internal carotid artery IMT |
rs601746 |
10 |
96,932,273 |
1.6 × 10-5 |
0.22 |
NEAR |
C10orf129 |
|
21 |
Ankle brachial index |
rs1905155 |
5 |
113,301,097 |
1.6 × 10-5 |
5.1 × 10-3 |
OUT |
|
|
22 |
Ankle brachial index |
rs10501784 |
11 |
91,592,192 |
1.6 × 10-5 |
0.30 |
OUT |
|
|
23 |
Ankle brachial index |
rs10493529 |
1 |
74,335,469 |
1.9 × 10-5 |
0.098 |
NEAR |
LRRC44, FPGT |
|
24 |
Common carotid artery IMT |
rs28207 |
5 |
13,267,852 |
1.9 × 10-5 |
2.1 × 10-4 |
OUT |
|
|
25 |
Abdominal aortic calcification |
rs8094641 |
18 |
59,873,880 |
2.0 × 10-5 |
0.04 |
NEAR |
C18orf20 |
|
26 |
Ankle brachial index |
rs2949535 |
18 |
26,111,783 |
2.0 × 10-5 |
7.5 × 10-4 |
OUT |
|
|
27 |
Coronary artery calcification |
rs2270861 |
12 |
100,238,849 |
2.0 × 10-5 |
6.8 × 10-3 |
IN |
DRIM |
|
28 |
Common carotid artery IMT |
rs853406 |
6 |
4,002,159 |
2.2 × 10-5 |
1.9 × 10-3 |
IN |
PRPF4B |
|
29 |
Common carotid artery IMT |
rs853407 |
6 |
4,002,232 |
2.2 × 10-5 |
2.5 × 10-3 |
IN |
PRPF4B |
|
30 |
Common carotid artery IMT |
rs1581413 |
3 |
158,532,867 |
2.2 × 10-5 |
1.8 × 10-3 |
IN |
VEPH1 |
|
|
||||||||
|
2b. Most significant results for FBAT analyses for multivariable-adjusted subclinical atherosclerosis measures |
||||||||
|
|
||||||||
|
FBAT rank |
Phenotype |
SNP |
Chr |
Physical location |
GEE P-value |
FBAT P-value |
Gene position |
Gene symbol |
|
|
||||||||
|
1 |
Common carotid artery IMT |
rs4814615 |
20 |
17,305,573 |
4.9 × 10-5 |
3.4 × 10-6 |
IN |
PCSK2 |
|
2 |
Common carotid artery IMT |
rs6053733 |
20 |
5,763,074 |
7.2 × 10-3 |
3.7 × 10-6 |
IN |
C20orf196 |
|
3 |
Ankle brachial index |
rs10499903 |
7 |
90,504,268 |
1.9 × 10-3 |
4.1 × 10-6 |
NEAR |
PFTK1, FZD1 |
|
4 |
Ankle brachial index |
rs9302997 |
17 |
71,723,439 |
4.8 × 10-3 |
5.1 × 10-6 |
IN |
RNF157 |
|
5 |
Ankle brachial index |
rs590183 |
4 |
23,733,535 |
0.01 |
8.6 × 10-6 |
OUT |
|
|
7 |
Ankle brachial index |
rs6832344 |
4 |
23,733,805 |
9.9 × 10-3 |
1.0 × 10-5 |
OUT |
|
|
8 |
Abdominal aortic calcification |
rs1023568 |
2 |
191,340,948 |
0.09 |
1.2 × 10-5 |
IN |
NAB1 |
|
9 |
Common carotid artery IMT |
rs2214959 |
12 |
124,674,521 |
0.01 |
1.5 × 10-5 |
NEAR |
TMEM132B |
|
10 |
Ankle brachial index |
rs9285151 |
13 |
42,712,236 |
0.06 |
1.7 × 10-5 |
IN |
ENOX1 |
|
11 |
Ankle brachial index |
rs1381632 |
4 |
88,926,163 |
0.36 |
1.8 × 10-5 |
NEAR |
DMP1 |
|
12 |
Coronary artery calcification |
rs4461066 |
16 |
51,469,110 |
8.7 × 10-3 |
3.1 × 10-5 |
OUT |
|
|
15 |
Coronary artery calcification |
rs367421 |
20 |
15,202,689 |
2.5 × 10-3 |
3.6 × 10-5 |
IN |
C20orf133 |
|
16 |
Internal carotid artery IMT |
rs9323431 |
14 |
62,638,241 |
0.24 |
3.6 × 10-5 |
IN |
KCNH5 |
|
17 |
Common carotid artery IMT |
rs1997463 |
3 |
54,782,280 |
0.01 |
3.8 × 10-5 |
IN |
CACNA2D3 |
|
19 |
Common carotid artery IMT |
rs304409 |
18 |
1,096,342 |
1.8 × 10-4 |
4.6 × 10-5 |
OUT |
|
|
21 |
Internal carotid artery IMT |
rs1349008 |
3 |
76,804,103 |
0.23 |
4.9 × 10-5 |
OUT |
|
|
22 |
Ankle brachial index |
rs2251671 |
8 |
40,501,973 |
1.3 × 10-4 |
4.9 × 10-5 |
NEAR |
ZMAT4 |
|
23 |
Abdominal aortic calcification |
rs243030 |
2 |
60,518,222 |
3.1 × 10-5 |
5.6 × 10-5 |
OUT |
|
|
24 |
Abdominal aortic calcification |
rs321967 |
7 |
77,959,200 |
4.7 × 10-4 |
6.0 × 10-5 |
IN |
MAGI2 |
|
25 |
Ankle brachial index |
rs6569792 |
6 |
132,736,444 |
0.56 |
6.4 × 10-5 |
IN |
MOXD1 |
|
26 |
Abdominal aortic calcification |
rs4985741 |
17 |
17,028,605 |
7.2 × 10-3 |
6.6 × 10-5 |
IN |
MRIP |
|
27 |
Ankle brachial index |
rs7995026 |
13 |
42,751,550 |
6.9 × 10-4 |
6.9 × 10-5 |
IN |
ENOX1 |
|
28 |
Coronary artery calcification |
rs10520541 |
4 |
184,055,754 |
0.08 |
7.0 × 10-5 |
IN |
AK001336 |
|
29 |
Internal carotid artery IMT |
rs2113945 |
15 |
29,111,823 |
0.09 |
7.2 × 10-5 |
IN |
TRPM1 |
|
30 |
Common carotid artery IMT |
rs6944400 |
7 |
131,389,740 |
0.12 |
8.2 × 10-5 |
OUT |
|
|
|
||||||||
|
2c. Genomic regions with LOD > 2.0 for linkage analyses for multivariable-adjusted subclinical atherosclerosis measures |
||||||||
|
|
||||||||
|
Rank |
Phenotype |
Marker |
Chr |
Physical location |
LOD score 1.5 interval bounds |
Maximum LOD |
||
|
|
||||||||
|
1 |
Internal carotid artery IMT |
ATA29A06 |
12 |
128,922,618 |
127,583,749 |
129,277,512 |
5.05 |
|
|
2 |
Internal carotid artery IMT |
rs959987 |
12 |
127,817,680 |
126,600,362 |
129,277,512 |
4.78 |
|
|
3 |
Internal carotid artery IMT |
rs1180937 |
1 |
54,903,665 |
45,417,474 |
56,950,040 |
4.23 |
|
|
8 |
Abdominal aortic calcification |
rs17030524 |
12 |
99,640,364 |
97,320,770 |
102,339,523 |
3.51 |
|
|
6 |
Coronary artery calcification |
SNP_A-1679277 |
6 |
149,300,408 |
136,476,887 |
154,228,170 |
2.81 |
|
|
7 |
Ankle brachial index |
rs394884 |
2 |
151,954,268 |
142,801,622 |
168,477,710 |
2.73 |
|
|
9 |
Internal carotid artery IMT |
rs300574 |
4 |
124,681,343 |
118,755,997 |
131,657,093 |
2.49 |
|
|
10 |
Internal carotid artery IMT |
rs714647 |
15 |
99,870,157 |
96,719,695 |
100,152,332 |
2.49 |
|
|
12 |
Coronary artery calcification |
rs1106679 |
14 |
102,555,405 |
91,636,556 |
106,312,036 |
2.33 |
|
|
13 |
Abdominal aortic calcification |
rs1454183 |
2 |
13,935,308 |
3,238,478 |
20,119,479 |
2.31 |
|
|
15 |
Coronary artery calcification |
rs7000744 |
8 |
140,003,669 |
136,360,837 |
146,039,126 |
2.23 |
|
|
16 |
Ankle brachial index |
rs10483084 |
21 |
42,268,393 |
40,113,290 |
45,025,009 |
2.12 |
|
|
17 |
Internal carotid artery IMT |
rs1948685 |
5 |
21,064,843 |
10,288,046 |
31,560,322 |
2.11 |
|
|
19 |
Internal carotid artery IMT |
rs10832008 |
11 |
13,232,905 |
6,384,682 |
19,637,706 |
2.09 |
|
|
|
||||||||
|
Abbreviations: SNP = single nucleotide polymorphism; Chr = chromosome; GEE = generalized estimating equations; FBAT = family based association testing; LOD = logarithm of the odds; IMT = intimal medial thickness;. Gaps appear in the rank order for markers that appear more than once. In the column entitled “Phenotype”, 'internal carotid artery IMT' denotes either mean or maximum internal carotid IMT, 'common carotid artery IMT' denotes either mean or maximum common carotid IMT, 'coronary artery calcification' denotes either mean CAC or max CAC, and 'ankle brachial index' denotes and ankle brachial index from either examination cycle 6 or cycle 7. For proximity to known genes (Table columns nine and ten), “IN” refers to a SNP within a protein-coding gene intron or exon, “OUT” refers to a SNP greater than 60 kb away from a protein-coding gene gene, and “NEAR” refer to a SNP within 60 kb of a protein-coding gene. |
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|
O'Donnell et al. BMC Medical Genetics 2007 8(Suppl 1):S4 doi:10.1186/1471-2350-8-S1-S4 |
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