Table 5.
CCREL, GIST, and Allele-Frequency Estimation for Families and Controls Typed at CIDR[Note]
|
P Value for Test |
|||||||||
|
Frequency in |
Moving-WindowHaplotype Test |
GIST |
|||||||
| SNP | Gene | Families(n=594) | Controls(n=179) | Allele Test | With 2 SNPs | With 3 SNPs | Genotype Test | NPL 10 | NPL 1 |
| rs6658788 | .460 | .489 | .37312 | .01616 | .00778 | .44415 | .106 | .055 | |
| rs1538687 | .234 | .307 | .00178 | .00206 | .00674 | .0054 | .781 | .129 | |
| rs1416962 | .321 | .352 | .16378 | .39256 | .4157 | .38009 | .566 | .019 | |
| rs946755 | .317 | .344 | .20073 | .20147 | <.00001 |
.37434 | .513 | .012 | |
| rs6428352 | .001 | .003 | … | <.00001 |
<.00001 |
… | … | … | |
| rs800292 | CFH | .132 | .232 | <.00001 |
<.00001 |
<.00001 |
<.00001 |
.437 | .001 |
| rs70620 | CFH | .147 | .173 | .15602 | <.00001 |
<.00001 |
.33122 | .893 | .333 |
| rs1853883 | .630 | .489 | <.00001 |
<.00001 |
<.00001 |
<.00001 |
.521 | <.001 |
|
| rs1360558 | .425 | .397 | .34842 | .60377 | .01118 | .63012 | .183 | .296 | |
| rs955927 | .416 | .391 | .36201 | .00833 | … | .65613 | .065 | .145 | |
| rs4350226 | .055 | .095 | .00182 | … | … | .00183 | .171 | .242 | |
| rs4752266 | GRK5 | .220 | .223 | .84131 | .23223 | .28973 | .03802 | .088 | .475 |
| rs915394 | GRK5 | .214 | .187 | .15214 | .19235 | .00309 | .35594 | .028 | .643 |
| rs1268947 | GRK5 | .112 | .117 | .97426 | .00969 | .01031 | .97976 | .052 | .345 |
| rs1537576 | GRK5 | .507 | .433 | .01881 | .01354 | .03257 | .0295 | .006 | .251 |
| rs2039488 | .078 | .115 | .01339 | .07877 | … | .05075 | .004 | .609 | |
| rs1467813 | RGS10 | .286 | .293 | .63177 | … | … | .71857 | .539 | .582 |
| rs927427 | .514 | .464 | .06936 | .00003 |
.00002 |
.05976 | .198 | .577 | |
| rs4146894 | PLEKHA1 | .598 | .466 | <.00001 |
<.00001 |
.00001 |
<.00001 |
.008 | .802 |
| rs1882907 | .127 | .187 | .00261 | .00013 |
.00006 |
.00521 | .169 | .172 | |
| rs760336 | PRSS11 | .395 | .480 | .00469 | .00126 | … | .02036 | .232 | .581 |
| rs763720 | PRSS11 | .295 | .212 | .00053 |
… | … | .00290 | .198 | .021 |
Note.— The minor-allele frequency is reported for controls (estimated by counting) and families (estimated by Mendel, version 5). Allele frequencies that differed between controls and families by >0.1 are in bold italics. For the allele test, the two-SNP and three-SNP moving-window haplotype tests, and the genotype test from the CCREL, P values ⩽.05 are in bold italics and P values ⩽.001 are underlined. The moving-window haplotype P values correspond to the SNPs in the same row as the P value and the next one or two SNPs for the two- and three-SNP moving window, respectively. For GIST, with the use of NPL scores from chromosome 1 (NPL 1) and chromosome 10 (NPL 10), P values ⩽.05 are in bold italics and P values ⩽.001 are underlined. Blank spaces separate the three chromosomal regions corresponding to SNPs in and around CFH, GRK5/RGS10, and PLEKHA1/LOC687715/PRSS11.