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) |
|---|---|---|---|---|---|---|---|
| (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 |
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.