Variant report
| Variant | rs13198716 |
|---|---|
| Chromosome Location | chr6:26582035-26582036 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:4)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:4 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr6:26201684..26204523-chr6:26580707..26582898,2 | K562 | blood: | |
| 2 | chr6:26161523..26164154-chr6:26581877..26584576,2 | K562 | blood: | |
| 3 | chr6:26580716..26583805-chr6:26585836..26589281,4 | K562 | blood: | |
| 4 | chr6:26581396..26586059-chr6:26589997..26593151,4 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000217275 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:30)
| rs_ID | r2[population] |
|---|---|
| rs13195509 | 0.83[CEU][hapmap];1.00[TSI][hapmap] |
| rs13201782 | 0.80[AMR][1000 genomes];0.80[EUR][1000 genomes] |
| rs13212985 | 0.91[AMR][1000 genomes];0.85[EUR][1000 genomes] |
| rs13220261 | 0.89[CEU][hapmap] |
| rs13220495 | 1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes] |
| rs2072803 | 1.00[YRI][hapmap] |
| rs2072806 | 1.00[YRI][hapmap] |
| rs2076030 | 1.00[YRI][hapmap] |
| rs2393667 | 1.00[YRI][hapmap] |
| rs34246779 | 0.91[AMR][1000 genomes] |
| rs34781270 | 0.91[AMR][1000 genomes];0.86[EUR][1000 genomes] |
| rs35076545 | 0.91[AMR][1000 genomes];0.86[EUR][1000 genomes] |
| rs35277236 | 0.91[AMR][1000 genomes] |
| rs35400317 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs35433030 | 0.91[AMR][1000 genomes] |
| rs36162392 | 0.91[AMR][1000 genomes];0.82[EUR][1000 genomes] |
| rs3734542 | 0.80[CEU][hapmap] |
| rs3823158 | 0.83[CEU][hapmap] |
| rs41266839 | 0.80[EUR][1000 genomes] |
| rs45527431 | 1.00[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs66488313 | 0.80[AMR][1000 genomes];0.84[EUR][1000 genomes] |
| rs66941101 | 0.91[AMR][1000 genomes] |
| rs67777156 | 0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes] |
| rs71557340 | 0.91[AMR][1000 genomes] |
| rs72843784 | 0.82[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs72845428 | 0.91[AMR][1000 genomes] |
| rs9358938 | 1.00[YRI][hapmap] |
| rs9366656 | 1.00[YRI][hapmap] |
| rs9379875 | 1.00[YRI][hapmap] |
| rs9393718 | 1.00[YRI][hapmap] |
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 | nsv1029920 | chr6:25638507-26585842 | Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 1215 gene(s) | inside rSNPs | diseases |
| 2 | nsv538162 | chr6:25638507-26585842 | Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 1215 gene(s) | inside rSNPs | diseases |
| 3 | nsv948921 | chr6:26556890-27443957 | Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 472 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:22)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs13198716 | BTN3A2 | cis | Muscle Skeletal | GTEx |
| rs13198716 | LOC100270746 | cis | lymphoblastoid | seeQTL |
| rs13198716 | BTN3A2 | cis | lymphoblastoid | GTEx |
| rs13198716 | BTN3A2 | cis | Esophagus Mucosa | GTEx |
| rs13198716 | BTN3A2 | cis | Nerve Tibial | GTEx |
| rs13198716 | BTN3A2 | cis | multi-tissue | Pritchard |
| rs13198716 | BTN3A2 | cis | lung | GTEx |
| rs13198716 | BTN3A2 | cis | Stomach | GTEx |
| rs13198716 | BTN3A2 | cis | lymphoblastoid | seeQTL |
| rs13198716 | BTN3A2 | cis | Thyroid | GTEx |
| rs13198716 | BTN3A2 | cis | uninvolved skin | skin_eQTL |
| rs13198716 | BTN3A2 | cis | Artery Tibial | GTEx |
| rs13198716 | BTN3A2 | cis | normal skin | skin_eQTL |
| rs13198716 | BTN3A2 | cis | Heart Left Ventricle | GTEx |
| rs13198716 | BTN3A2 | cis | Artery Aorta | GTEx |
| rs13198716 | BTN3A2 | cis | Esophagus Muscularis | GTEx |
| rs13198716 | BTN3A2 | cis | Adipose Subcutaneous | GTEx |
| rs13198716 | BTN3A2 | cis | Whole Blood | GTEx |
| rs13198716 | BTN3A3 | cis | lymphoblastoid | seeQTL |
| rs13198716 | BTN3A2 | Cis_1M | lymphoblastoid | RTeQTL |
| rs13198716 | BTN3A2 | cis | Skin Sun Exposed Lower leg | GTEx |
| rs13198716 | BTN3A2///BTN3A3 | Cis_1M | lymphoblastoid | RTeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr6:26581400-26584600 | Enhancers | K562 | blood |
