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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.