Table 4.
In silico predictions for the significantly associated variants replicated in this study
| Reference | Locus | SNP | Annotated Gene (RefSeq) |
Annotated Gene (GENCODE) |
No. of SNPs with r2 > 0.8 |
Promoter Histone Marks | Enhancer Histone Marks | DNAse | Motifs changed | eQTLhits | RelevanteQTL tissue1(Correlatedgene) | Relevant P-value of eQTL1 | Relevant eQTL tissue2 (Correlated gene) | Relevant P-value of eQTL2 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diouf | 14q21.1 | rs8014839 | FBXO33 | CTAGE5 | 3 | 8 tissues (Brain) | 13 tissues (Brain) | Skin, Liver, MUS, VAS | 2 altered motifs | 4 hits | Blood (CTAGE5) | 4.68 × 10−54 | Blood (TRAPPC6B) | 2.80 × 10−43 |
| Diouf | 4q28.1 | rs4618330 | INTU | RP11-123G5.1 | 11 | MUS | 12 altered motifs | – | – | – | ||||
| Baldwin | 3q27.3 | rs1903216 | BCL6 | RP11-44H4.1 | 1 | GI | 5 tissues | 5 altered motifs | – | – | – | |||
| Diouf | 3p14.2 | rs35558909 | FHIT | FHIT | 2 | ESDR, Blood | 6 altered motifs | – | – | – | ||||
| Diouf | 3p21.1 | rs4687753 | IL17RB | IL17RB | 49 | Breast | ESDR, Blood, Brain | 8 altered motifs | 53 hits | Tibial nerve (ACTR8) | 1.78 × 10−12 | Tibial nerve (CHDH) | 1.06 × 10−7 | |
| Diouf | 8q24.12 | rs7817522 | DEPTOR | DEPTOR | 11 | IPSC, Fat, GI | GI, Brain | ESDR, MUS | 1 altered motifs | 5 hits | Brain (DEPTOR) | 8.06 × 10−6 | Esophagus Muscularis (DEPTOR) | 6.43 × 10− 7 |
| Schneider | 15q21.3 | rs2062640 | UNC13C | UNC13C | 23 | – | – | – | – | – | ||||
| Diouf | 2q33.3 | rs11694118 | LOC100507443 | snoU13 | 27 | STRM | Placenta, Brain | 1 altered motifs | ||||||
| Diouf | 5q23.2 | rs6891783 | ZNF608 | CTD-2308B18.3 | 38 | IPSC, Lung, Brain | STRM, Fat, MUS, THYM | Lung | 2 altered motifs | – | – | – | – | – |
Functional annotations from the ENCODE based HaploReg v4.1 tool (http://www.broadinstitute.org/mammals/haploreg/haploreg.php) and eQTL analysis according to GTEx Portal (http://www.gtexportal.org/home/)
Chr Chromosome, SNP Single nucleotide polymorphism, LD Linkage disequilibrium, eQTL Expression quantitative trait loci, DNAse deoxyribonuclease, MUS Skletal muscle, VAS Vascular system, GI Gastro intestinal system, ESDR Embryonic stem cell derivatives, ESC Embryonic stem cells, IPSC Induced pluripotent stem cells, STRM Mesenchymal stem cell derived chondrocyte cultured cells