Table 2

SNPs identified for various cohorts using the stringent filter (Part 1).

Cohort(s)

SNP/identity

(degeneracy)

Chr: Pos. (hg17)

and orientation

Duplicon

length

Characterized genes and

pseudogenes in duplicons


CD

rs4471699

16:

30.2 M→

147 kb

SULT1A3, GIYD2, BOLA2, IMAA, CORO1A

99.6%

16:

29.4 M→

146 kb

SULT1A3, GIYD2, BOLA2, IMAA, MLAS

98.1%

16:

21.8 M→

41 kb

[UQCRC2]

98.0%

16:

22.3 M←

42 kb

[NPIPL3]

98.0%

16:

21.3 M→

42 kb

IMAA, [NPIPL3]

97.1%

16:

18.8 M→

75 kb

SMG1

RA

rs669980

9:

0.2 M→

193 kb

CBWD1, FOXD4, FAM138A, WASH1, [DOCK8]

98.9% (F)

2:

114 M←

189 kb

CBWD2, FOX4DL1, FAM138B, WASH2P, [RABL2A]

CAD, T2D

rs10502407

18:

10.6 M→

52 kb

-

97.9%

18:

12.2 M←

64 kb

[CIDEA]

CAD

rs12134625

1:

78 M→

931

-

97.0%

1:

24 M←

932

FUSIP1

BD, CAD

rs9551988

13:

19.2 M→

2.6 kb

PSPC1

HT

96.2% (F)

13:

18.7 M→

2.8 kb

[TUBA3C]

HT

rs935019

2:

127,162 K→

3.6 kb

GYPC

95.3% (F)

2:

127,166 K→

3.5 kb

GYPC

HT

rs12227938

12:

37 M→

154 kb

ALG10B

95.3% (P)

12:

34 M→

127 kb

ALG10

T2D

SNP_A-1797773

16:

45 M→

14 kb

VPS35, [ORC6L]

94.8% (F)

16:

34 M←

16 kb

-

T1D

rs12381130

16:

5 M→

88 kb

ALG1, FAM86A

94.7%

3:

127 M←

76 kb

ALG1L

94.6%

11:

67 M→

79 kb

-

94.6%

11:

71 M←

40 kb

FAM86C, [DEFB108B]

94.5%

11:

3 M→

91 kb

[ZNF195]

94.3%

3:

76 M→

44 kb

[FAM86D]

94.0%

4:

9 M←

120 kb

-

93.9%

3:

131 M→

44 kb

-

93.9%

4:

4 M→

53 kb

-

93.7%

12:

8 M→

53 kb

[FAM90A1]

93.6%

8:

12 M→

41 kb

[FAM86B1]

93.5%

8:

8 M←

63 kb

-


Multiple almost-contiguous segmental duplications are treated as a single large duplicon (intervening sequence is included in the length). The table includes only duplicons with at least 85% identity to the region containing the SNP. Duplicons with identical flanking sequence to the SNP are labeled as fully degenerate (F); duplicons with partial degeneracy are labeled (P). Characterized genes are listed if they occur within a duplicon. Genes in square brackets are outside the duplicon, but the duplicon is at most 30 kb upstream of the gene. Genes for a SNP are italicized if the SNP is within that gene, or if the SNP maps to a position within that gene in the duplicon.

Ross BMC Medicine 2011 9:12   doi:10.1186/1741-7015-9-12

Open Data