Variant report
| Variant | rs461311 |
|---|---|
| Chromosome Location | chr1:112654994-112654995 |
| allele | G/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr1:112653652..112656343-chr1:112664473..112666963,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:37)
| rs_ID | r2[population] |
|---|---|
| rs12751286 | 1.00[ASN][1000 genomes] |
| rs1372861 | 1.00[ASN][1000 genomes] |
| rs1443925 | 1.00[ASN][1000 genomes] |
| rs171994 | 0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs17739527 | 1.00[ASN][1000 genomes] |
| rs2819209 | 0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs3008534 | 1.00[ASN][1000 genomes] |
| rs3017628 | 1.00[ASN][1000 genomes] |
| rs34751177 | 1.00[ASN][1000 genomes] |
| rs35143807 | 0.80[AMR][1000 genomes] |
| rs367572 | 1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs371188 | 0.80[AMR][1000 genomes] |
| rs373157 | 1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs374902 | 1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs374958 | 1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs400151 | 1.00[ASN][1000 genomes] |
| rs4088223 | 1.00[ASN][1000 genomes] |
| rs430680 | 0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs432663 | 1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs434800 | 1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs436173 | 1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs436818 | 0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs441740 | 1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs443625 | 1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs450822 | 0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs455228 | 1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs457342 | 0.81[EUR][1000 genomes] |
| rs460443 | 1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs461553 | 0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs462936 | 1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs463983 | 1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs464357 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs464819 | 1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs466206 | 0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs4838935 | 1.00[ASN][1000 genomes] |
| rs609882 | 0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7413702 | 1.00[CHD][hapmap] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv831048 | chr1:112459697-112680279 | Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 24 gene(s) | inside rSNPs | diseases |
| 2 | nsv831059 | chr1:112569062-112724725 | Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh | Chromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| 3 | nsv831070 | chr1:112594658-112792539 | Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | diseases |
| 4 | nsv1000467 | chr1:112641655-112659834 | Weak transcription Active TSS Enhancers | Chromatin interactive region | n/a | inside rSNPs | diseases |
mRNA abundance (count:6)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs461311 | RSBN1 | cis | parietal | SCAN |
| rs461311 | RHOC | cis | lymphoblastoid | seeQTL |
| rs461311 | NHLH2 | cis | parietal | SCAN |
| rs461311 | DRAM2 | cis | parietal | SCAN |
| rs461311 | LOC642864 | cis | cerebellum | SCAN |
| rs461311 | LOC100216001 | trans | lymphoblastoid | seeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:112654400-112655000 | Enhancers | Stomach Mucosa | stomach |
