|
Genotype and allele frequencies of 39 polymorphisms in CAPN1 |
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| SNP |
Position |
AA change |
Genotypes and number of animal |
Minor allele frequency |
Heterozygosity |
HWE** |
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|
|
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| c.579G>A* |
Exon5 |
K193K |
G (187) |
AG (177) |
A (53) |
0.339 |
0.448 |
0.276 |
| c.630A>G* |
Exon6 |
T210T |
A (174) |
AG (180) |
G (67) |
0.373 |
0.468 |
0.078 |
| c.657C>T |
Exon6 |
G219G |
C (13) |
CT (5) |
T (5) |
0.326 |
0.44 |
0.015 |
| c.760-24T>C* |
Intron6 |
. |
T (210) |
CT (161) |
C (43) |
0.298 |
0.419 |
0.148 |
| c.843+96T>C |
Intron7 |
. |
T (10) |
CT (12) |
C (2) |
0.333 |
0.444 |
0.54 |
| c.843+161T>A |
Intron7 |
. |
T (10) |
AT (12) |
A (2) |
0.333 |
0.444 |
0.54 |
| c.843+195T>C |
Intron7 |
. |
T (10) |
CT (12) |
C (2) |
0.333 |
0.444 |
0.54 |
| c.843+269T>C |
Intron7 |
. |
T (10) |
CT (12) |
C (2) |
0.333 |
0.444 |
0.54 |
| c.843+288C>T |
Intron7 |
. |
C (10) |
CT (12) |
T (2) |
0.333 |
0.444 |
0.54 |
| c.843+323C>T |
Intron7 |
. |
C (13) |
CT (5) |
T (5) |
0.326 |
0.44 |
0.015 |
| c.843+330A>G* |
Intron7 |
. |
A (224) |
AG (156) |
G (31) |
0.265 |
0.39 |
0.596 |
| c.1199G>A* |
Exon11 |
R400Q |
G (417) |
AG (3) |
A (0) |
0.004 |
0.007 |
0.941 |
| c.1588G>A* |
Exon14 |
V530I |
G (289) |
AG (111) |
A (15) |
0.17 |
0.282 |
0.293 |
| c.1611+104C>T* |
Intron14 |
. |
C (227) |
CT (155) |
T (33) |
0.266 |
0.391 |
0.369 |
| c.1611+515G>A |
Intron14 |
. |
G (20) |
AG (1) |
A (0) |
0.024 |
0.046 |
0.911 |
| c.1736-164CCTinsdel |
Intron16 |
. |
del (19) |
insdel (4) |
ins (1) |
0.125 |
0.219 |
0.243 |
| c.1736-40A>G |
Intron17 |
. |
A (19) |
AG (4) |
G (1) |
0.125 |
0.219 |
0.243 |
| c.1800+169C>T |
Intron17 |
. |
C (16) |
CT (5) |
T (2) |
0.196 |
0.315 |
0.138 |
| c.1800+195G>A |
Intron17 |
. |
G (19) |
AG (4) |
A (1) |
0.125 |
0.219 |
0.243 |
| c.1869+60G>A |
Intron18 |
. |
G (19) |
AG (4) |
A (1) |
0.125 |
0.219 |
0.243 |
| c.1869+82A>G |
Intron18 |
. |
A (19) |
AG (4) |
G (1) |
0.125 |
0.219 |
0.243 |
| c.1869+91T>G |
Intron18 |
. |
T (19) |
GT (4) |
G (1) |
0.125 |
0.219 |
0.243 |
| c.1869+235G>C* |
Intron18 |
. |
C (128) |
CG (189) |
G (102) |
0.469 |
0.498 |
0.053 |
| c.2065+46A>G |
Intron20 |
. |
A (19) |
AG (4) |
G (1) |
0.125 |
0.219 |
0.243 |
| c.2065+68G>A |
Intron20 |
. |
G (19) |
AG (4) |
A (1) |
0.125 |
0.219 |
0.243 |
| c.2124+19Cinsdel |
Intron21 |
. |
ins (23) |
insdel (1) |
del (0) |
0.021 |
0.041 |
0.917 |
| c.2124+23T>G |
Intron21 |
. |
T (23) |
GT (1) |
G (0) |
0.021 |
0.041 |
0.917 |
| c.2124+74G>A |
Intron21 |
. |
G (22) |
AG (2) |
A (0) |
0.042 |
0.08 |
0.831 |
| c.2148G>A |
Exon22 |
A716A |
G (22) |
AG (2) |
A (0) |
0.042 |
0.08 |
0.831 |
| c.2151*479C>T* |
3'UTR |
. |
C (342) |
CT (65) |
T (5) |
0.091 |
0.165 |
0.345 |
| c.2151*503Tinsdel |
3'UTR |
. |
ins (22) |
insdel (2) |
del (0) |
0.042 |
0.08 |
0.831 |
| c.2151*550T>G |
3'UTR |
. |
T (19) |
GT (3) |
G (0) |
0.068 |
0.127 |
0.731 |
| c.2151*557T>C |
3'UTR |
. |
T (19) |
CT (3) |
C (0) |
0.068 |
0.127 |
0.731 |
| c.2151*562C>A |
3'UTR |
. |
C (20) |
AC (2) |
A (0) |
0.045 |
0.087 |
0.823 |
| c.2151*578CTCCCTCCinsdel |
3'UTR |
. |
ins (19) |
insdel (3) |
del (0) |
0.068 |
0.127 |
0.731 |
| c.2151*697T>C |
3'UTR |
. |
T (19) |
CT (3) |
C (0) |
0.068 |
0.127 |
0.731 |
| c.2151*765A>G* |
3'UTR |
. |
A (307) |
AG (96) |
G (12) |
0.145 |
0.247 |
0.187 |
| c.2151*832G>A* |
3'UTR |
. |
G (335) |
AG (75) |
A (4) |
0.1 |
0.18 |
0.931 |
| c.2151*845A>G* |
3'UTR |
. |
A (293) |
AG (112) |
G (12) |
0.163 |
0.273 |
0.744 |
|
*Frequencies of the six polymorphisms marked by asterisks were determined by genotyping 421 Korean native cattle. Frequencies of the remaining polymorphisms were determined by re-sequencing 24 unrelated Korean native cattle DNAs. ** P-values of deviation from Hardy-Weinberg equilibrium | ||||||||
Cheong et al. BMC Genetics 2008 9:33 doi:10.1186/1471-2156-9-33 |
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