Table 6.
CCREL, GIST, and Allele-Frequency Estimation for Locally Typed Families and Controls[Note]
|
P Value for Test |
|||||||||
|
Frequency in |
Moving-WindowHaplotype Test |
GIST |
|||||||
| SNP | Gene | Families(n=323) | Controls(n=117) | Allele Test | With 2 SNPs | With 3 SNPs | Genotype Test | NPL 10 | NPL 1 |
| rs6658788 | .563 | .483 | .02200 | .00052 |
.00162 | .04920 | .319 | .244 | |
| rs1538687 | .213 | .342 | .00004 |
.00043 |
.00066 |
.00014 |
.652 | .302 | |
| rs1416962 | .299 | .393 | .00597 | .02623 | .02051 | .01819 | .442 | .041 | |
| rs946755 | .295 | .380 | .01234 | .01243 | <.00001 |
.04531 | .409 | .040 | |
| rs6428352 | .001 | .004 | … | <.00001 |
<.00001 |
… | … | … | |
| rs800292 | CFH | .120 | .269 | <.00001 |
<.00001 |
<.00001 |
<.00001 |
.315 | .014 |
| rs1061170 | CFH | .609 | .310 | <.00001 |
<.00001 |
<.00001 |
<.00001 |
.895 | .132 |
| rs10922093 | CFH | .210 | .295 | .00693 | .00175 | <.00001 |
.01723 | .360 | .327 |
| rs70620 | CFH | .148 | .150 | .91163 | <.00001 |
<.00001 |
.56770 | .737 | .356 |
| rs1853883 | .633 | .432 | <.00001 |
<.00001 |
<.00001 |
<.00001 |
.776 | .011 | |
| rs1360558 | .437 | .389 | .18014 | .43576 | .02079 | .37993 | .975 | .488 | |
| rs955927 | .433 | .385 | .15343 | .01037 | … | .36087 | .017 | .585 | |
| rs4350226 | .050 | .103 | .00312 | … | … | .00373 | .228 | .174 | |
| rs4752266 | GRK5 | .223 | .226 | .81772 | .27748 | .64917 | .08279 | .107 | .453 |
| rs915394 | GRK5 | .228 | .209 | .34489 | .83219 | .05560 | .62183 | .049 | .320 |
| rs1268947 | GRK5 | .117 | .115 | .81975 | .02748 | .02192 | .78965 | .049 | .689 |
| rs1537576 | GRK5 | .497 | .419 | .02604 | .02232 | .05636 | .06334 | .012 | .023 |
| rs2039488 | .083 | .115 | .11177 | .42428 | … | .42399 | .025 | .358 | |
| rs1467813 | RGS10 | .293 | .295 | .86608 | … | … | .85954 | .506 | .492 |
| rs927427 | .506 | .487 | .56710 | .00056 |
.00083 |
.42264 | .306 | .625 | |
| rs4146894 | PLEKHA1 | .611 | .474 | .00004 |
.00012 |
.00053 |
.00024 |
.006 | .737 |
| rs12258692 | PLEKHA1 | .008 | .000 | … | .54750 | .00018 |
… | … | … |
| rs4405249 | PLEKHA1 | .139 | .158 | .39378 | .00026 |
.00280 | .33118 | .003 | .345 |
| rs1045216 | PLEKHA1 | .289 | .427 | .00004 |
.00036 |
.00001 |
.00026 |
.068 | .825 |
| rs1882907 | .131 | .184 | .01761 | .00140 | .01099 | .04401 | .017 | .372 | |
| rs10490923 | LOC387715 | .089 | .141 | .02112 | .05024 | <.00001 |
.03415 | .086 | .251 |
| rs2736911 | LOC387715 | .121 | .119 | .71668 | <.00001 |
<.00001 |
.64230 | .312 | .968 |
| rs10490924 | LOC387715 | .475 | .193 | <.00001 |
<.00001 |
<.00001 |
<.00001 |
.018 | .327 |
| rs11538141 | PRSS11 | .004 | .005 | … | .00726 | .01676 | … | … | … |
| rs760336 | PRSS11 | .373 | .474 | .00527 | .01386 | .00036 |
.01396 | .479 | .683 |
| rs763720 | PRSS11 | .296 | .226 | .01645 | .00016 |
… | .03899 | .305 | .451 |
| rs1803403 | PRSS11 | .118 | .030 | .00009 |
… | … | .00022 |
.714 | .778 |
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. Locally typed SNPs are in bold italics. Blank spaces separate the three chromosomal regions corresponding to SNPs in and around CFH, GRK5/RGS10, and PLEKHA1/LOC687715/PRSS11.