Table 1

SNPs, genes and microsatellites analysed in this study

SNP identity

Chromosome

Gene

Microsatellite name

Microsatellite distance from SNP (kb)

H-W

DH/sd

PS

PE


rs1009127

1

LRRC7 (leucine rich repeat 7)

LRRC-1

+34.6

NS

-3.6

0.007

NS

rs718830

7

CFTR (cystic fibrosis transmembrane conductance regulator)

IVS8CA*

+14.5

NS

-4.7

0.003

0.03

IVS17B*

+49.2

NS

-1.1

NS

NS

CFTR-3

-10.2

NS

-1.3

NS

NS

rs997929

8

TOX (thymus high mobility group box protein)

TOX-1

-20.4

-

-

-

-

TOX-2

+22.2

NS

-1.2

NS

NS

rs726733

11

SYT9 (synaptotagmin IX)

SYT9-1

-7

NS

-2.8

0.019

NS

SYT9-2

+40.9

NS

-1.4

NS

NS

rs1111108

14

PKCη (protein kinase C, eta)

PRKCH-1

+8.7

NS

-6.3

0.0001

0.016

PRKCH-2

-70.4

NS

-6.6

0.0001

0.013

rs761057

16

TPSG1 (γ-triptase 1)

TPSG-1

-74.3

NS

1.5

0.001

0.003

TPSG-2

+41.4

NS

-0.2

NS

NS

rs998262

5

No gene

NG-1

-4.6

p = 0.04

-5.2

0.0001

0.022

NG-2

+31.7

NS

-3.6

0.008

NS

rs902336

1

32 kb upstream from the

ABCD3-1

-15.7

NS

-3.2

0.015

NS

gene ABCD3

ABCD3-2

-2

-

-

-

-


'SNP identity' indicates the identification number of each SNP as annotated in dbSNP NCBI (National Center for Biotechnology Information). 'Chromosome' indicates on which chromosome the SNP is located. 'Gene' indicates the gene in which the SNP is located or the nearest gene in the case of the last SNP. 'Microsatellite name' is the name given to the microsatellites flanking the SNP; the same name can be found in Figure 3, where the microsatellites are placed in the genome-wide distribution. 'Microsatellite distance from the SNP' is the distance (in kilobase) upstream (+) or downstream (-) between the microsatellite and the SNP. These statistics are reported from analyses carried out on the microsatellite data. 'H-W' is the p value from the Hardy-Weinberg equilibrium test. 'DH/sd' is the observed gene diversity minus the expected heterozygosity (DH) according the Ewens-Watterson's statistic divided by the standard deviation (sd) of the gene diversity (see the text for details). 'PS' is the significance of the difference between observed gene diversity and expected heterozygosity resulting from the simulation carried out by the program BOTTLENECK. 'PE' is the significance calculated using the empirical distribution; only values < 0.05 are quoted. NS, not significant. The two microsatellites marked with an asterisk have been described previously [19,20] and no data for the two markers that were not scorable are denoted by hyphens.

Mattiangeli et al. Genome Biology 2006 7:R74   doi:10.1186/gb-2006-7-8-r74

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