Defining the contribution of SNPs identified in asthma GWAS to clinical variables in asthmatic children

BMC Medical Genetics

Table 5 Analysis of key GWAS SNPs with data from ENCODE

SNP	Gene locus/location	Number of SNPs in LD (r² = 1) (no.)	GERP Conservation	Enhancer histone marks (no. of SNPs in regions)	DNase (no. of SNPs in regions)	Proteins bound (no. of SNPs in regions)	Motifs changed (no. of SNPs with motif changed regions)
SNP	Gene locus/location	Number of SNPs in LD (r² = 1) (no.)	(no. of SNPs conserved)	Enhancer histone marks (no. of SNPs in regions)	DNase (no. of SNPs in regions)	Proteins bound (no. of SNPs in regions)	Motifs changed (no. of SNPs with motif changed regions)
rs2305480 C/T	GSDMB/Ser311Pro	26	2	3	1	0	14
rs11078927 C/T	GSDMB/intronic	26	2	3	1	0	14
rs1342326 T/G	IL33/5′-region	7	0	1	2	2	4
rs3939286 G/A	IL33/5′-region	1	0	0	0	0	1
rs3771166 C/T	IL18R1/intronic	16	0	2	1	0	9
rs1420101 G/A	IL1RL1/intronic	6	1	2	1	1	1
rs744910 A/G	SMAD3/intronic	3	0	1	2	2	1
rs2284033 A/G	IL2RB/intronic	3	0	0	3	0	1
rs1588265 A/G	PDE4D/intronic	14	2	0	1	0	5
rs2786098 C/A	CRB1/intronic	11	0	0	3	0	7
rs2244012 A/G	RAD50/intronic	51	2	6	9	5	25

The 11 SNPs genotyped as part of this study were entered into the HaploReg tool to investigate whether SNPs in the same LD block were likely to affect chromatin structure and regulatory element binding motifs.

ISSN: 1471-2350