Table 3

SNP Associations with a GEE or FBAT p-value < 0.001 for selected phenotype and p values < 0.01 for at least two other phenotypes within selected group of related phenotypes

Selected Phenotype : (p < 0.001)

SNP

Chr

Physical Position

Gene

MRI phenotype showing strongest association with SNP

GEE p-value


TCBV

rs646860

1

60310322

C1orf87

APBV

6.5 × 10-4

TCBV

rs7763081

6

53816274

LRRC1

ATCBV

6.5 × 10-4

TCBV

rs1444644

12

20457227

PDE3A

ATBV

8.8 × 10-5

TCBV

rs10505865

12

20453861

PDE3A

AFBV

1.4 × 10-4

TCBV

rs1444645

12

20457264

PDE3A

ATBV

1.8 × 10-4

TCBV

rs1444629

12

20454174

PDE3A

ATCBV

2.7 × 10-4

TCBV

rs303816

12

50469752

SCN8A

ATCBV

6.1 × 10-4

TCBV

rs2827980†

21

23524857

ATCBV

5.9 × 10-5

TCBV

rs9297594†

8

120287483

AFBV

1.3 × 10-4

TCBV

rs10512927†

5

50346833

ATCBV

8.5 × 10-4


Selected Phenotype : (p < 0.001)

SNP

Chr

Physical Position

Gene

Phenotype showing strongest association with SNP

FBAT p-value


TCBV

rs7740148

6

35063681

ANKS1

AFBV

0.003

TCBV

rs6496742

15

89324040

PRC1

ATCBV

6.4 × 10-4

TCBV

rs2788646

1

66518974

PDE4B

ATCBV

3.3 × 10-4

TCBV

rs10500956†

11

23435031

AFBV

0.003

TCBV

rs2059943†

8

107140783

ATCBV

1.4 × 10-4

TCBV

rs853256†

3

64290504

AFBV

7.5 × 10-4

TCBV

rs853260†

3

64289592

AFBV

4.4 × 10-4


Selected Phenotype : (p < 0.001)

SNP

Chr

Physical Position

Gene

Phenotype showing strongest association with SNP

GEE p-value


F1

rs4733809

8

1.29E+08

TMEM75

Sim

1.5 × 10-4

F1

rs3923615

11

24638108

LUZP2

F1

1.1 × 10-4

F1

rs10515155

17

53836943

RNF43

F1

3.6 × 10-

F1

rs1204116

6

62462055

KHDRBS2

F1

7.3 × 10-4

F1

rs708891

12

1.18E+08

CCDC60

F1

4.7 × 10-4

F1

rs10515159

17

54157692

RAD51C

F1

3.1 × 10-4

F1

rs10506214

12

41397957

F3

5.8 × 10-4

F3

rs608825

1

2.33E+08

EDARADD

F3

5.5 × 10-4

F3

rs957603

15

38796960

RAD51

F3

1.5 × 10-4

F3

rs10506214†

12

41397957

F3

5.8 × 10-4

F3

rs2109479

5

56979996

F3

4.2 × 10-4


Table is ordered by primary phenotype (TCBV, F1 or F3; whether significant phenotype-SNP association was based on GEE or FBAT p-value and then alphabetically by gene name.

* Genes in bold and highlighted in discussion; † SNPs were not within 60 KB of a known gene.

Seshadri et al. BMC Medical Genetics 2007 8(Suppl 1):S15   doi:10.1186/1471-2350-8-S1-S15

Open Data