Variant report
| Variant | rs10874778 |
|---|---|
| Chromosome Location | chr1:93866169-93866170 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
| No data |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:29)
| rs_ID | r2[population] |
|---|---|
| rs10874777 | 0.87[ASN][1000 genomes] |
| rs11164916 | 0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs11164924 | 0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs11576494 | 0.82[ASN][1000 genomes] |
| rs12044883 | 0.82[ASN][1000 genomes] |
| rs12124771 | 0.86[AFR][1000 genomes] |
| rs12133576 | 0.82[ASN][1000 genomes] |
| rs12133907 | 0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs12138486 | 1.00[ASN][1000 genomes] |
| rs12406245 | 0.87[ASN][1000 genomes] |
| rs12752223 | 0.80[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs1426318 | 0.86[ASN][1000 genomes] |
| rs1559828 | 0.82[ASN][1000 genomes] |
| rs1593512 | 0.87[ASN][1000 genomes] |
| rs2114273 | 0.84[AMR][1000 genomes];0.84[ASN][1000 genomes] |
| rs2391256 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs35102250 | 0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes] |
| rs3767962 | 0.80[EUR][1000 genomes];0.82[ASN][1000 genomes] |
| rs3767964 | 0.82[ASN][1000 genomes] |
| rs4847240 | 0.82[ASN][1000 genomes] |
| rs4847412 | 0.82[ASN][1000 genomes] |
| rs4847419 | 0.86[ASN][1000 genomes] |
| rs4847420 | 0.86[ASN][1000 genomes] |
| rs59417472 | 0.86[ASN][1000 genomes] |
| rs6658257 | 0.82[AMR][1000 genomes];0.82[ASN][1000 genomes] |
| rs6680022 | 0.83[ASN][1000 genomes] |
| rs6694508 | 0.83[ASN][1000 genomes] |
| rs7417952 | 0.87[ASN][1000 genomes] |
| rs7525248 | 0.82[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv871640 | chr1:93807122-93953469 | Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 31 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:8)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs10874778 | DR1 | Cis_1M | lymphoblastoid | RTeQTL |
| rs10874778 | TMED5 | Cis_1M | lymphoblastoid | RTeQTL |
| rs10874778 | RP4-717I23.3 | cis | Artery Tibial | GTEx |
| rs10874778 | RP4-717I23.3 | cis | Nerve Tibial | GTEx |
| rs10874778 | RP4-717I23.3 | cis | lung | GTEx |
| rs10874778 | RP4-717I23.3 | cis | Muscle Skeletal | GTEx |
| rs10874778 | RP4-717I23.3 | cis | Adipose Subcutaneous | GTEx |
| rs10874778 | RP4-717I23.3 | cis | Skin Sun Exposed Lower leg | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:93865600-93867000 | Enhancers | Placenta Amnion | Placenta Amnion |
| 2 | chr1:93865800-93866400 | Enhancers | Placenta | Placenta |
| 3 | chr1:93866000-93866400 | Enhancers | H1 BMP4 Derived Trophoblast Cultured Cells | ES cell derived |
