Variant report
| Variant | rs12121203 |
|---|---|
| Chromosome Location | chr1:159230865-159230866 |
| allele | A/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:35)
| rs_ID | r2[population] |
|---|---|
| rs10489848 | 0.85[ASN][1000 genomes] |
| rs10489854 | 0.87[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes] |
| rs10489855 | 0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes] |
| rs11265146 | 0.85[ASN][1000 genomes] |
| rs11265164 | 0.92[ASN][1000 genomes] |
| rs12087219 | 0.87[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes] |
| rs12561917 | 0.85[ASN][1000 genomes] |
| rs12564837 | 0.93[ASN][1000 genomes] |
| rs12568101 | 0.85[ASN][1000 genomes] |
| rs16841967 | 0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes] |
| rs16841970 | 0.83[YRI][hapmap] |
| rs2269718 | 0.81[JPT][hapmap] |
| rs2269719 | 0.82[JPT][hapmap] |
| rs2325914 | 0.82[ASN][1000 genomes] |
| rs2325915 | 0.91[ASN][1000 genomes] |
| rs2325924 | 0.84[AMR][1000 genomes];0.99[EUR][1000 genomes] |
| rs2875781 | 0.93[ASN][1000 genomes] |
| rs3027055 | 0.90[ASN][1000 genomes] |
| rs3027056 | 0.90[ASN][1000 genomes] |
| rs3027061 | 0.90[ASN][1000 genomes] |
| rs3027063 | 0.90[ASN][1000 genomes] |
| rs3027074 | 0.85[ASN][1000 genomes] |
| rs3027075 | 0.85[ASN][1000 genomes] |
| rs3027077 | 0.85[ASN][1000 genomes] |
| rs34497749 | 0.85[ASN][1000 genomes] |
| rs34757892 | 0.85[ASN][1000 genomes] |
| rs35014997 | 0.85[ASN][1000 genomes] |
| rs35262301 | 0.85[ASN][1000 genomes] |
| rs35921532 | 0.90[ASN][1000 genomes] |
| rs3845624 | 0.99[ASN][1000 genomes] |
| rs3893415 | 0.80[YRI][hapmap] |
| rs4498802 | 0.85[ASN][1000 genomes] |
| rs59012264 | 0.84[AMR][1000 genomes];0.99[EUR][1000 genomes] |
| rs60069993 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs72633670 | 0.93[ASN][1000 genomes] |
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 | nsv872487 | chr1:159196765-159342439 | Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 6 gene(s) | inside rSNPs | diseases |
| 2 | nsv872488 | chr1:159218266-159336948 | Flanking Active TSS Enhancers Weak transcription Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 6 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:4)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs12121203 | C1orf189 | cis | cerebellum | SCAN |
| rs12121203 | ETV3L | cis | cerebellum | SCAN |
| rs12121203 | B4GALT3 | cis | parietal | SCAN |
| rs12121203 | CD48 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:159230600-159231400 | Enhancers | HMEC | breast |
| 2 | chr1:159230600-159233200 | Enhancers | NHEK | skin |
| 3 | chr1:159230800-159231400 | Enhancers | Foreskin Keratinocyte Primary Cells skin03 | Skin |
| 4 | chr1:159230800-159232800 | Enhancers | Foreskin Keratinocyte Primary Cells skin02 | Skin |
