Variant report
| Variant | rs6746402 |
|---|---|
| Chromosome Location | chr2:100150443-100150444 |
| 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:41)
| rs_ID | r2[population] |
|---|---|
| rs10173883 | 1.00[CHB][hapmap] |
| rs10179697 | 1.00[CHB][hapmap] |
| rs10180138 | 1.00[CHB][hapmap] |
| rs10180688 | 1.00[CHB][hapmap] |
| rs10186223 | 1.00[CHB][hapmap] |
| rs10191001 | 1.00[CHB][hapmap] |
| rs10207435 | 1.00[CHB][hapmap] |
| rs10210257 | 1.00[CHB][hapmap] |
| rs10210346 | 1.00[CHB][hapmap] |
| rs10496337 | 1.00[CHB][hapmap] |
| rs11123784 | 1.00[CHB][hapmap] |
| rs13028722 | 1.00[CHB][hapmap] |
| rs13401163 | 1.00[CHB][hapmap] |
| rs13409359 | 1.00[CHB][hapmap] |
| rs13415713 | 1.00[CHB][hapmap] |
| rs13416265 | 1.00[CHB][hapmap] |
| rs13419448 | 1.00[CHB][hapmap] |
| rs13426758 | 1.00[CHB][hapmap] |
| rs13427251 | 0.88[CEU][hapmap];0.86[EUR][1000 genomes] |
| rs13429185 | 1.00[CHB][hapmap] |
| rs13429806 | 1.00[CHB][hapmap] |
| rs13430962 | 1.00[CHB][hapmap] |
| rs13431410 | 1.00[CHB][hapmap] |
| rs13432046 | 1.00[CHB][hapmap] |
| rs1376444 | 0.80[ASN][1000 genomes] |
| rs1882598 | 1.00[CHB][hapmap] |
| rs1901284 | 0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2309577 | 1.00[CHB][hapmap] |
| rs3087399 | 1.00[CHB][hapmap] |
| rs3828162 | 1.00[CHB][hapmap] |
| rs4851212 | 0.84[MEX][hapmap];0.80[AMR][1000 genomes] |
| rs6712137 | 1.00[CHB][hapmap] |
| rs6726711 | 1.00[CHB][hapmap] |
| rs7569805 | 1.00[CHB][hapmap] |
| rs7579143 | 1.00[CHB][hapmap] |
| rs7582085 | 1.00[CHB][hapmap] |
| rs7582133 | 1.00[CHB][hapmap] |
| rs7599384 | 1.00[CHB][hapmap] |
| rs9308819 | 1.00[CHB][hapmap] |
| rs9308821 | 1.00[CHB][hapmap] |
| rs9308822 | 1.00[CHB][hapmap] |
Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv431424 | chr2:99652682-100494682 | Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 49 gene(s) | inside rSNPs | diseases |
| 2 | nsv962113 | chr2:100022168-100317461 | Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 16 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:12)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs6746402 | AFF3 | cis | cerebellar cortex | BrainEAC |
| rs6746402 | TSGA10 | cis | cerebellum | SCAN |
| rs6746402 | LIPT1 | cis | parietal | SCAN |
| rs6746402 | REV1 | Cis_1M | lymphoblastoid | RTeQTL |
| rs6746402 | AFF3 | cis | temporal cortex | BrainEAC |
| rs6746402 | ARID5A | cis | parietal | SCAN |
| rs6746402 | LIPT1 | Cis_1M | lymphoblastoid | RTeQTL |
| rs6746402 | LIPT1 | cis | cerebellum | SCAN |
| rs6746402 | FAM178B | cis | cerebellum | SCAN |
| rs6746402 | AFF3 | cis | frontal cortex | BrainEAC |
| rs6746402 | AFF3 | cis | brain | BrainEAC |
| rs6746402 | TSGA10 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr2:100144000-100152400 | Weak transcription | Spleen | Spleen |
| 2 | chr2:100146800-100154600 | Weak transcription | H1 Derived Mesenchymal Stem Cells | ES cell derived |
