Variant report
| Variant | rs2007748 |
|---|---|
| Chromosome Location | chr2:211357642-211357643 |
| allele | A/C/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 | chr2:211341728..211344856-chr2:211357164..211360434,3 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000021826 | Chromatin interaction |
| ENSG00000115365 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:19)
| rs_ID | r2[population] |
|---|---|
| rs10932334 | 0.89[CEU][hapmap] |
| rs10932339 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes] |
| rs12694202 | 0.82[JPT][hapmap] |
| rs12694203 | 0.81[JPT][hapmap] |
| rs1509820 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes] |
| rs2042049 | 0.91[YRI][hapmap] |
| rs2287418 | 0.89[CEU][hapmap] |
| rs2287420 | 0.89[CEU][hapmap];0.91[YRI][hapmap] |
| rs2287603 | 1.00[CHB][hapmap];0.90[JPT][hapmap] |
| rs2370948 | 0.92[YRI][hapmap] |
| rs2370961 | 0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs2370998 | 0.82[JPT][hapmap] |
| rs3755182 | 0.89[CEU][hapmap];0.91[YRI][hapmap] |
| rs58133833 | 0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs60112891 | 0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs6712000 | 0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs7573258 | 0.81[JPT][hapmap] |
| rs7580046 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7603241 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | esv3398091 | chr2:211315261-211634200 | Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 12 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:4)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs2007748 | CPS1 | cis | lung | GTEx |
| rs2007748 | CPS1 | cis | Skin Sun Exposed Lower leg | GTEx |
| rs2007748 | CPS1 | cis | Adipose Subcutaneous | GTEx |
| rs2007748 | LANCL1 | Cis_1M | lymphoblastoid | RTeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr2:211343400-211363600 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
| 2 | chr2:211352200-211361000 | Weak transcription | H9 Derived Neuronal Progenitor Cultured Cells | ES cell derived |
