Variant report
| Variant | rs1354171 |
|---|---|
| Chromosome Location | chr5:50231548-50231549 |
| allele | C/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 | chr5:50228151..50230751-chr5:50231157..50233024,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000251601 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:20)
| rs_ID | r2[population] |
|---|---|
| rs17217942 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs173648 | 0.81[AFR][1000 genomes] |
| rs192223 | 0.88[AFR][1000 genomes] |
| rs1993954 | 1.00[YRI][hapmap];0.93[AFR][1000 genomes] |
| rs250225 | 0.88[AFR][1000 genomes] |
| rs250226 | 0.85[AFR][1000 genomes] |
| rs250227 | 1.00[YRI][hapmap];0.85[AFR][1000 genomes] |
| rs250228 | 1.00[YRI][hapmap];0.85[AFR][1000 genomes] |
| rs250231 | 1.00[YRI][hapmap];0.85[AFR][1000 genomes] |
| rs250232 | 0.91[YRI][hapmap];0.81[AFR][1000 genomes] |
| rs250235 | 0.91[YRI][hapmap];0.81[AFR][1000 genomes] |
| rs250240 | 0.85[AFR][1000 genomes] |
| rs250241 | 0.85[AFR][1000 genomes] |
| rs250243 | 1.00[YRI][hapmap];0.85[AFR][1000 genomes] |
| rs27276 | 0.86[AFR][1000 genomes] |
| rs31714 | 0.88[AFR][1000 genomes] |
| rs589372 | 0.85[AFR][1000 genomes] |
| rs602484 | 0.85[AFR][1000 genomes] |
| rs614328 | 0.85[AFR][1000 genomes] |
| rs630982 | 0.81[AFR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1034445 | chr5:49986171-50492609 | Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 16 gene(s) | inside rSNPs | diseases |
| 2 | nsv598116 | chr5:50064292-50318550 | Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 11 gene(s) | inside rSNPs | diseases |
| 3 | nsv830286 | chr5:50165805-50374600 | Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 10 gene(s) | inside rSNPs | diseases |
| 4 | nsv1034194 | chr5:50209649-50234259 | Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive region | 1 gene(s) | inside rSNPs | diseases |
| 5 | nsv511286 | chr5:50231548-50254200 | Enhancers | TF binding regionChromatin interactive region | 2 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs1354171 | TMCC3 | trans | parietal | SCAN |
| rs1354171 | SRSF5 | trans | parietal | SCAN |
Chromatin state (count:0 , 50 per page) page:
| No data |
