Table 4 SNPs that are in LD with associated haplotype

From: Genome-wide analysis of genetic susceptibility to language impairment in an isolated Chilean population

SNP

Chr posn

D′ nuc Fams

D′ Confidence Intervals

LOD nuc Fams

R 2 nuc Fams

D′ Fam5

D′ Confidence Intervals

LOD Fam5

R 2 Fam5

Genes

Peak of Linkage?

rs2040587

114 462 759

0.23

0.04–0.44

0.66

0.04

0.50

0.27–0.66

2.99

0.14

300 kb downstream of FOXP2

 

rs1962522

134 436 889

0.48

0.25–0.65

2.77

0.17

0.39

0.20–0.54

2.69

0.14

AGBL3

 

rs10488598

136 238 383

0.56

0.28–0.76

2.58

0.11

0.53

0.21–0.73

1.74

0.10

CHRM2

 

rs1371463

137 933 620

0.46

0.26–0.62

3.32

0.15

0.31

0.10–0.49

1.39

0.07

SVOPL

 

rs1464798

138 982 540

0.64

0.36–0.81

3.25

0.15

0.62

0.39–0.77

4.26

0.20

HIPK2

 

rs1476640

141 058 779

0.10

0.00–0.31

0.17

0.01

0.27

0.05–0.48

0.74

0.04

WEE2

Peak of parametric linkage

rs768055

141 059 520

0.80

0.47–0.93

3.61

0.17

0.76

0.34–0.91

2.04

0.12

WEE2

Peak of parametric linkage

rs727714

143 729 925

1.00

0.88–1.00

18.1

0.67

1.00

0.92–1.00

23.1

0.70

NOBOX (exon 3)

Associated haplotype SNP

rs969356

143 804 256

1.00

0.89–1.00

19.8

0.71

1.00

0.91–1.00

21.5

0.65

TPK1

Associated haplotype SNP

rs802200

145 736 404

0.42

0.23–0.58

3.00

0.17

0.39

0.18–0.55

2.21

0.13

CNTNAP2

 

rs1524341

146 337 622

0.23

0.05–0.41

0.87

0.05

0.21

0.04–0.37

0.78

0.04

CNTNAP2

Peak of non-parametric linkage

rs1024676

146 346 794

0.22

0.03–0.43

0.52

0.03

0.23

0.03–0.45

0.51

0.03

CNTNAP2

Peak of non-parametric linkage

rs4431523

147 228 099

0.45

0.23–0.63

2.66

0.12

0.38

0.15–0.57

1.7

0.07

CNTNAP2

 
  1. Abbreviations: Chr, chromosome; posn, position; SNP, single nucleotide polymorphism.
  2. Any SNP that has a D′>0.4 and a pairwise LOD>2.0 with the associated haplotype is shown. Measures of LD were evaluated both in nuclear families and in the extended pedigree as shown in Figure 1.
  3. The associated haplotype was formed from SNPs rs727714 and rs969356. These two SNPs gave the maximum NPL score of the non-parametric linkage analyses using allele frequencies from all genotyped individuals. The peak of linkage in the non-parametric analyses using allele frequencies from founder and CEPH individuals fell across SNPs rs1524341 whereas the peak of parametric linkage fell at SNPs rs1476640 and rs760885.
  4. All SNPs are intronic unless otherwise stated.
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