A genome-wide approach to identify genetic loci with a signature of natural selection in the Irish population

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	P_S	P_E
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). 'P_S' is the significance of the difference between observed gene diversity and expected heterozygosity resulting from the simulation carried out by the program BOTTLENECK. 'P_E' 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.

ISSN: 1474-760X