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Table 5 Analysis of key GWAS SNPs with data from ENCODE

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

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)
(no. of SNPs conserved)
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
  1. 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.