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Table 6 Analysis of the GSDMB LD block (r 2 =1) using data from ENCODE

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

SNP Gene locus/location Chromosomal location (hg19) GERP conservation (Y/N) Enhancer histone marks DNase Proteins bound Motifs changed
rs12709365 A/G ZPBP2/intronic 17:38027400 N GM12878 N N N
rs13380815 A/G ZPBP2/intronic 17:38027583 N GM12878 N N N
rs11870965 T/A ZPBP2/intronic 17:38030205 N N N N Myb
rs10852935 C/T ZPBP2/synonymous 17:38031674 Y N N N N
rs10852936 C/T ZPBP2/intronic 17:38031714 N N N N Foxp1, Foxq1
rs36095411 T/G ZPBP2/intronic 17:38031865 N N N N 9 motifs altered
rs34189114 C/T ZPBP2/intronic 17:38032460 N N N N N
rs35736272 T/C ZPBP2/intronic 17:38032680 Y N N N N
rs9907088 G/A ZPBP2/downstream 17:38035116 N N N N Sox
rs36038753 G/T ZPBP2/downstream 17:38035370 N N N N Dobox4
rs35569035 C/T ZPBP2/downstream 17:38036524 N N N N Pax4
rs9904624 A/G ZPBP2/downstream 17:38036586 N N N N N
rs12232497 T/C Intergenic 17:38040119 N N N N N
rs12232498 T/C Intergenic 17:38040363 N N N N Lhx3
rs12941333 C/T Intergenic 17:38040534 N N N N Pou3f3, Pou2f1
rs2872507 G/A Intergenic 17:38040763 N N N N N
rs12936409 C/T Intergenic 17:38043649 N N N N N
rs8069176 G/A GSDMB/downstream 17:38057197 N N N N Gfi1, Mafk, Pax4
rs4795399 T/C GSDMB/intronic 17:38061439 N HepG2 Huh7.5,CMK N Pxx6, Pax
rs2305480 G/A GSDMB /Ser311Pro 17:38062196 N N N N N
rs62067034 C/T GSDMB/intronic 17:38063738 N N N N SREBP, LXR
rs11078927 C/T GSDMB /intronic 17:38064405 N N N N N
rs11078928 T/C GSDMB/intronic 17:38064469 N N N N Foxp1
rs4795400 C/T GSDMB/intronic 17:38067020 N N N N N
rs77749396 G/C GSDMB/intronic 17:38073840 N N N N ZNF219
rs9303279 G/C GSDMB/intronic 17:38073968 N N N N Obox3
  1. The two GSDMB SNPs genotyped as part of this study (rs2305480 and rs110788927) were part of a wider LD block containing 26 SNPs in total spanning 46,568 bp. These SNPs were analysed using HaploReg to see if they atlered any binding sites for regulatory elements or other proteins and also whether they affected chromatin states and their conservation according to GERP. The CEU frequency from 1000 Genomes Project =0.48 for all SNPs. CMK: human leukaemic cell line; GERP genomic evolutionary rate profiling score; GM12878: lymphoblastoid cell line; GSDMB gasdermin-domain containing protein family B; HepG2: human hepatocellular liver carcinoma cell line; Huh7.5: human hepatocellular cell line; ZPBP2 zona pellucid binding protein 2 gene. SNPs genotyped in the current study are shown in bold.