Table 1.
Segregation test of 34 variants in family 242
| Chrom:Positiona | Ref | Alt | Gene | dbSNP | 1000Gb | Co-441 | Co-634 | Co-666 | Co-667 | Co-771 | Co-652 | Co-692 | Co-657 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1:235577776 | C | T | TBCE | rs62620041 | 0.0023 | C/T | C/C | C/T | C/T | C/T | C/C | C/C | C/C |
| 2:29295186 | C | T | C2orf71 | rs75276619 | 0.01 | C/T | C/T | C/T | C/C | C/C | C/C | C/T | C/C |
| 2:155555406 | A | G | KCNJ3 | rs16838016 | 0.0032 | A/G | A/A | A/G | A/G | A/G | A/G | A/A | A/G |
| 2:169870004 | G | A | ABCB11 | rs11568361 | A/G | G/G | A/G | A/G | A/G | A/G | G/G | G/G | |
| 3:137786409 | A | C | DZIP1L | A/C | A/C | A/C | A/C | A/C | A/C | A/A | A/C | ||
| 3:142542415 | C | T | PCOLCE2 | rs147612568 | 0.0014 | C/T | C/T | C/T | C/T | C/T | C/T | C/C | C/T |
| 3:151171329 | G | T | IGSF10 | rs143721392 | G/T | G/T | G/T | G/T | G/T | G/T | G/T | G/T | |
| 3:151598890 | T | C | SUCNR1 | C/T | C/T | C/T | C/T | C/T | C/T | C/T | C/T | ||
| 4:13590380 | A | G | BOD1L1 | rs140964488 | 0.0009 | A/G | A/G | A/G | A/A | A/G | A/A | A/G | A/A |
| 4:22440018 | C | G | GPR125 | rs144997202 | 0.0005 | C/G | C/G | C/G | C/C | C/G | C/G | C/G | C/C |
| 4:25849449 | G | A | SEL1L3 | A/G | A/G | A/G | G/G | A/G | A/G | A/G | G/G | ||
| 7:141765172 | A | T | MGAM | A/T | A/T | A/T | A/A | A/T | A/A | A/A | A/A | ||
| 9:107331452 | G | A | OR13C8 | A/G | A/G | A/G | A/G | A/G | G/G | G/G | G/G | ||
| 9:111947836 | GGA | - | EPB41L4B | GGA/- | GGA/- | GGA/- | GGA/- | GGA/- | GGA/GGA | GGA/GGA | GGA/GGA | ||
| 9:139369066 | G | A | SEC16A | rs148167113 | 0.01 | A/G | A/G | A/G | A/G | A/G | A/G | A/G | A/G |
| 9:139401233 | C | T | NOTCH1 | rs61751543 | 0.01 | C/T | C/T | C/T | C/T | C/T | C/T | C/T | C/T |
| 10:5931230 | C | T | ANKRD16 | rs3750659 | 0.06 | C/T | C/T | C/T | C/C | C/T | C/C | C/C | C/C |
| 11:130784886 | T | C | SNX19 | rs117260465 | 0.01 | C/T | C/T | C/T | T/T | C/T | T/T | C/T | T/T |
| 12:10954583 | A | T | TAS2R7 | rs139604652 | 0.0032 | A/T | A/T | A/T | A/T | A/T | A/A | A/T | A/A |
| 12:109617728 | A | G | ACACB | rs16940029 | 0.08 | A/G | A/A | A/G | A/A | A/G | A/A | A/G | A/G |
| 16:14029033 | G | A | ERCC4 | rs1800067 | 0.03 | A/G | G/G | A/G | A/G | A/G | G/G | G/G | A/G |
| 16:15818842 | A | G | MYH11 | rs16967510 | 0.02 | A/G | A/A | A/G | A/A | A/G | A/G | A/A | A/G |
| 16:22826046 | T | G | HS3ST2 | rs189013090 | 0.01 | G/T | T/T | G/T | G/T | G/T | T/T | T/T | G/T |
| 17:62028920 | C | G | SCN4A | rs41280102 | 0.01 | C/G | C/C | C/G | C/C | C/G | G/G | C/G | C/G |
| 18:67721492 | G | C | RTTN | rs34717557 | 0.01 | C/G | G/G | C/G | G/G | C/G | C/G | G/G | C/G |
| 18:67836115 | G | T | RTTN | rs34353615 | 0.01 | G/T | G/G | G/T | G/G | G/T | G/T | G/G | G/T |
| 18:72343156 | A | G | ZNF407 | rs75994611 | 0.01 | A/G | A/A | A/G | A/A | A/G | A/G | A/A | A/G |
| 19:3834863 | C | T | ZFR2 | rs61747120 | 0.04 | C/T | C/C | C/T | C/C | C/T | C/T | C/T | C/T |
| 22:30733787 | C | T | SF3A1 | C/T | C/T | C/T | C/T | C/T | C/T | C/T | C/C | ||
| 22:30951208 | C | T | GAL3ST1 | rs139452633 | 0.0005 | C/T | C/T | C/T | C/T | C/T | C/T | C/T | C/C |
| 22:38111897 | C | T | TRIOBP | rs143157673 | 0.0018 | C/T | C/T | C/T | C/T | C/T | C/T | C/T | C/C |
| 22:46653273 | C | T | PKDREJ | rs147180698 | C/T | C/C | C/T | C/C | C/T | C/T | C/T | C/C | |
| X:107844666 | G | T | COL4A5 | rs34077552 | 0.01 | G/T | G/G | G/T | G/T | T/T | G/T | G/T | G/T |
| X:119293216 | - | G | RHOXF2 | -/G | −/− | -/G | -/G | -/G | -/G | -/G | -/G |
List of 34 rare variants after filtering all non-exonic variants, synonymous variants, variants presenting in the 30 breast cancer cases [15], and variants with allele frequency in 1000Genomes more than 20 %
aGRCh37 (hg19) coordinates
b1000 Genomes version April 2012 (hg19)