Variant report
| Variant | rs254617 |
|---|---|
| Chromosome Location | chr5:52446274-52446275 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:1)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
| No data |
(count:1 , 50 per page) page:
1
| No. | lncRNA name | Chromosome Location | lncRNA alias |
|---|---|---|---|
| 1 | lnc-ITGA2-3 | chr5:52445214-52446721 | l_2918_chr5:52441399-52446721_testes |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:11)
| rs_ID | r2[population] |
|---|---|
| rs152944 | 0.90[AMR][1000 genomes];0.94[EUR][1000 genomes] |
| rs1823072 | 0.94[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs251331 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs251335 | 0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs251336 | 0.94[AMR][1000 genomes];0.94[EUR][1000 genomes] |
| rs251337 | 0.94[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs251338 | 0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs254614 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs254618 | 0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs30088 | 0.94[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs30093 | 0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][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 | nsv949005 | chr5:52188028-52808229 | Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 35 gene(s) | inside rSNPs | diseases |
| 2 | esv2752745 | chr5:52422063-53343529 | Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 22 gene(s) | inside rSNPs | diseases |
| 3 | nsv980563 | chr5:52436848-52446366 | Inactive region | lncRNA | n/a | inside rSNPs | diseases |
| No data |
Chromatin state (count:0 , 50 per page) page:
| No data |
