Variant report
| Variant | rs6699343 |
|---|---|
| Chromosome Location | chr1:47867739-47867740 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
| No data |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:57)
| rs_ID | r2[population] |
|---|---|
| rs10157883 | 0.86[JPT][hapmap] |
| rs10399673 | 0.95[JPT][hapmap] |
| rs10437097 | 0.90[EUR][1000 genomes] |
| rs10789507 | 0.86[JPT][hapmap] |
| rs10890475 | 0.86[JPT][hapmap] |
| rs10890478 | 0.85[JPT][hapmap] |
| rs11211504 | 0.86[JPT][hapmap] |
| rs11211508 | 0.86[JPT][hapmap];0.81[TSI][hapmap] |
| rs11211513 | 0.86[JPT][hapmap] |
| rs11211517 | 0.90[JPT][hapmap] |
| rs11211520 | 0.85[JPT][hapmap] |
| rs11582877 | 0.86[JPT][hapmap] |
| rs12039726 | 0.89[CEU][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes] |
| rs12090153 | 0.82[JPT][hapmap] |
| rs12407746 | 0.81[EUR][1000 genomes] |
| rs2405922 | 0.90[JPT][hapmap] |
| rs2406102 | 0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs2406105 | 0.81[EUR][1000 genomes] |
| rs2472725 | 0.90[JPT][hapmap] |
| rs2622925 | 0.90[JPT][hapmap] |
| rs2622927 | 0.81[GIH][hapmap] |
| rs2742104 | 0.86[JPT][hapmap] |
| rs2758735 | 0.86[JPT][hapmap] |
| rs2820971 | 0.90[JPT][hapmap] |
| rs2820983 | 0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs2820989 | 0.90[JPT][hapmap] |
| rs2821088 | 0.86[JPT][hapmap] |
| rs2821093 | 0.90[JPT][hapmap] |
| rs3088062 | 0.89[CEU][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap] |
| rs3122607 | 0.86[JPT][hapmap] |
| rs3122611 | 0.86[JPT][hapmap] |
| rs3122615 | 0.85[JPT][hapmap] |
| rs3122619 | 0.86[JPT][hapmap] |
| rs3125624 | 0.86[JPT][hapmap] |
| rs3125628 | 0.85[JPT][hapmap] |
| rs3125630 | 0.86[JPT][hapmap] |
| rs3125632 | 0.81[JPT][hapmap] |
| rs3125633 | 0.90[JPT][hapmap] |
| rs3125635 | 0.86[JPT][hapmap];0.81[TSI][hapmap] |
| rs3125636 | 0.84[JPT][hapmap] |
| rs3125644 | 0.85[JPT][hapmap];0.80[TSI][hapmap] |
| rs3814003 | 0.83[CEU][hapmap] |
| rs3925058 | 0.86[JPT][hapmap] |
| rs4492666 | 0.85[JPT][hapmap] |
| rs4603175 | 0.95[JPT][hapmap] |
| rs4926836 | 0.86[JPT][hapmap] |
| rs6588348 | 0.90[JPT][hapmap] |
| rs6660321 | 0.89[CEU][hapmap];0.86[JPT][hapmap] |
| rs6662189 | 0.85[EUR][1000 genomes] |
| rs6671254 | 0.86[JPT][hapmap] |
| rs6673882 | 0.95[JPT][hapmap] |
| rs6679121 | 1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs6697248 | 0.86[JPT][hapmap];0.81[TSI][hapmap] |
| rs7525650 | 0.90[JPT][hapmap] |
| rs7532148 | 0.86[JPT][hapmap] |
| rs9436430 | 0.90[JPT][hapmap] |
| rs9436882 | 0.86[JPT][hapmap] |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs6699343 | SNORD38A | cis | cerebellum | SCAN |
| rs6699343 | CMPK1 | cis | lymphoblastoid | seeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:47847600-47872800 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
| 2 | chr1:47866600-47869200 | Enhancers | Fetal Intestine Large | intestine |
| 3 | chr1:47866600-47869200 | Enhancers | Fetal Intestine Small | intestine |
| 4 | chr1:47867400-47868400 | Enhancers | Stomach Mucosa | stomach |
