Table 2.
Variants associated with increased risk to endemic pemphigus foliaceus.
| Association analyses | Predicted eQTL of the associated SNPs and their proxy | |||||
|---|---|---|---|---|---|---|
|
SNP Genomic position* |
Location | Model |
OR (95% CI) p‐value |
Affected gene | Cell, tissue or organ |
Effect p‐value |
| B‐cell modulation | ||||||
|
rs6657275*G Chr1:218596461 |
Intron of TGFB2 | Rec |
2.26 (1.33‐3.84) p = 2.6x10−3 |
TGFB2 | Lung, testis, brain | eQTL<8.2x10−3 |
| TGFB2‐AS1 | Whole blood, skeletal muscle | eQTL<2.8x10−9 | ||||
| V(D)J rearrangement | ||||||
| rs1818545*A Chr11:36612090 | Intergenic between RAG1, RAG2 and IFTAP | Dom |
1.85 (1.22‐2.81) p = 3.6 x10−3 |
IFTAP | Brain | eQTL<7.1x10−3 |
|
rs10781530*A Chr9:139885948 |
921 bp 5’ of PAXX | Add |
1.58 (1.16‐2.15) p = 3.6x10−3 |
PAXX | Whole blood, lung, heart, brain, artery, adipose | eQTL<8.9x10−5 |
| Class‐switch recombination and somatic hypermutation | ||||||
|
rs10870140*G Chr9:139796419 |
Intron of TRAF2 | Rec |
1.76 (1.19‐2.61) p = 4.9x10−3 |
TRAF2 | Whole blood | eQTL<1.2x10−9 |
| PAXX | Brain | eQTL<6.5 x10−6 | ||||
|
rs10781522*A Chr9:139815053 |
Intron of TRAF2 | Add |
1.61 (1.22‐2.14) p = 9x10−3 |
TRAF2 | Whole blood, transverse colon, testis, lymphoblastoid cell, monocytes, skeletal muscle, skin, tibial nerve, dendritic cells | eQTL<3.5 x10−4 |
| Rec |
1.99 (1.30‐3.05) p = 1.5x10−3 |
PAXX | Blood, brain | eQTL<1.2 x10−3 | ||
|
rs535068*A Chr1:12189561 |
Intron of TNFRSF8 | Dom |
3.11 (1.46‐6.62) p = 3.2x10−3 |
TNFRSF1B | Whole blood, skin, brain | eQTL<3.1 x10−3 |
|
rs324011*A Chr12:57502182 |
Intron of STAT6 | Add |
1.56 (1.16‐2.10) p = 3.3x10−3 |
STAT6 | Whole blood, CD4+ lymphocytes, monocytes, brain, liver, colon sigmoid | eQTL<1.4 x10−4 |
| Dom |
1.94 (1.30‐2.90) p = 1.3x10−3 |
|||||
|
rs2070729*C Chr5:131819921 |
Intron of IRF1 | Add |
1.56 (1.17‐2.09) p = 2.8x10−3 |
IRF1 | Whole blood, heart, monocytes | eQTL<4.7 x10−4 |
| Rec |
2.02 (1.25‐3.27) p = 4.4x10−3 |
IRF1‐AS1 | Whole blood, thyroid, spleen, skin, tibial nerve, Skeletal muscle, lung, heart, oesophagus, colon, brain, artery, adipose | eQTL<1.1 x10−4 | ||
| IL13 | Tibial nerve | eQTL<4.2 x10−5 | ||||
|
rs6432018*C Chr2:9721896 |
2.2 kb 3’ of YWHAQ | Add |
1.69 (1.28‐2.24) p = 3x10−3 |
YWHAQ | Tibial artery | sQTL<1.3 x10−6 |
| Dom |
2.04 (1.32‐3.14) p = 1.2 x10−3 |
|||||
|
rs17149161*C Chr7:75978229 |
intron of YWHAG | Add |
1.63 (1.20‐2.21) p = 1.7 x10−3 |
YWHAG | Monocytes, adipose, lung | eQTL<1.6 x10−4 |
SNP: rs ID of the single nucleotide polymorphism, Chr: chromosome, OR: odds ratio, CI: confidence interval. eQTL: expression quantitative trait loci. *Genomic position according to GRCh37.p13 primary assembly. The frequency of the associated alleles in patients and controls is given in Table S3. The complete list of proxy SNPs is available in Table S5.