Variant report
| Variant | rs7554853 |
|---|---|
| Chromosome Location | chr1:169380254-169380255 |
| allele | C/T |
| 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:33)
| rs_ID | r2[population] |
|---|---|
| rs10489190 | 1.00[ASN][1000 genomes] |
| rs10494478 | 1.00[ASN][1000 genomes] |
| rs10919149 | 1.00[ASN][1000 genomes] |
| rs10919150 | 1.00[ASN][1000 genomes] |
| rs10919153 | 1.00[ASN][1000 genomes] |
| rs10919158 | 1.00[ASN][1000 genomes] |
| rs10919162 | 1.00[ASN][1000 genomes] |
| rs10919165 | 1.00[ASN][1000 genomes] |
| rs10919172 | 0.93[ASN][1000 genomes] |
| rs12022617 | 1.00[ASN][1000 genomes] |
| rs12022768 | 0.93[ASN][1000 genomes] |
| rs12025397 | 0.93[ASN][1000 genomes] |
| rs12025721 | 1.00[ASN][1000 genomes] |
| rs12028208 | 0.93[ASN][1000 genomes] |
| rs12037926 | 1.00[ASN][1000 genomes] |
| rs12044982 | 1.00[ASN][1000 genomes] |
| rs12401962 | 1.00[ASN][1000 genomes] |
| rs12402774 | 0.93[ASN][1000 genomes] |
| rs1517742 | 0.93[ASN][1000 genomes] |
| rs1517746 | 0.93[ASN][1000 genomes] |
| rs17345531 | 1.00[ASN][1000 genomes] |
| rs17349677 | 1.00[ASN][1000 genomes] |
| rs17518147 | 0.93[ASN][1000 genomes] |
| rs17576927 | 0.93[ASN][1000 genomes] |
| rs1949426 | 0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2092083 | 0.93[ASN][1000 genomes] |
| rs3766100 | 1.00[ASN][1000 genomes] |
| rs3766101 | 1.00[ASN][1000 genomes] |
| rs72704035 | 0.93[ASN][1000 genomes] |
| rs72706084 | 0.86[ASN][1000 genomes] |
| rs7414819 | 0.86[ASN][1000 genomes] |
| rs7522565 | 0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs7546361 | 0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | esv10418 | chr1:169059628-169621268 | Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 56 gene(s) | inside rSNPs | diseases |
| 2 | nsv872531 | chr1:169191860-169388193 | Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 9 gene(s) | inside rSNPs | diseases |
| 3 | nsv831871 | chr1:169320673-169486680 | Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 28 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs7554853 | NME7 | cis | Thyroid | GTEx |
| rs7554853 | NME7 | Cis_1M | lymphoblastoid | RTeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:169360800-169395200 | Weak transcription | Brain Dorsolateral Prefrontal Cortex | brain |
