Details of rs2395185
A summary of the functionality scores for this SNP
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Functional categories with no record for this SNP are omitted and will not be displayed in the following individual sections
Sequential information
Sequential information of the SNP obtained from NCBI dbSNP and allele frequencies in five continental population obtained from 1000 Genomes Phase 3 (final phase)
| Variant ID | Chr | Position | MAF | Ref/Alt | EAS | AMR | AFR | EUR | SAS |
|---|---|---|---|---|---|---|---|---|---|
| None | None | None | None | None | None | None | None | None | None |
Visualization
The circular and linear plots of chromatin loops, states and signatures associated to the SNP using CIRCOS
and UCSC Genome Browser
Population genetic statistics
Integrated haplotype scores (iHS) and Fixation index (Fst) for five continental population obtained from 1000 Genomes Phase 3 (final phase)
| Statistics | AMR | EUR | EAS | SAS | AFR |
|---|---|---|---|---|---|
| None | None | None | None | None | None |
ClinVar
ClinVar aggregates information about genomic variation and its relationship to human health.
| ClinVarID | Condition | Database | Intepretation | Sequence Ontology | Gene | Origin |
|---|---|---|---|---|---|---|
| None | None | None | None | None | None | None |
Candidate cis-regulatory elements
The status of open chromatin for over 750,000 candidate cis-regulatory elements (cCREs) in 54 distinct cell types.
| Position | Tissue | Mapping ratio | cCREs |
|---|---|---|---|
| None | None | None | None |
| Position | Tissue | Mapping ratio | cCREs |
eQTL
Significant SNP-gene pairs (FDR < 0.05) associated to the SNP in 44 human tissues obtained from GTEx Portal
| Gene | P-value | Effect size | Tissue |
|---|---|---|---|
| None | None | None | None |
| Gene | P-value | Effect size | Tissue |
Three-dimensional interacting SNP
Genetically associated SNPs (LD r2 > 0.8) interacting with the SNP through 3D chromatin loops
| Variant ID | Population | LD(r2) | Loop type | Loop start | Loop end | Distance | Cell type | Tissue |
|---|---|---|---|---|---|---|---|---|
| None | None | None | None | None | None | None | None | None |
| Variant ID | Population | LD(r2) | Loop type | Loop start | Loop end | Distance | Cell type | Tissue |
Chromatin state
Presented chromatin state identified by the Core 15-state ChromHMM model
| Chromatin state | Cell type | Tissue | Description |
|---|---|---|---|
| None | None | None | None |
| Chromatin state | Cell type | Tissue | Description |
Transcription factor binding site
Transcription factor binding sites identified by ChIP-seq in ENCODE project
| Transcription Factor | Cell type | Tissue | DNA accessibility |
|---|---|---|---|
| None | None | None | None |
| Transcription Factor | Cell type | Tissue | DNA accessibility |
Sequence motif altered
Altered TF binding motifs by the SNP via scanning the genome using the TRANSFAC
and JASPAR databases
| Source | Motif | Strand | Matched sequence | Ref | Alt | Motif logo |
|---|---|---|---|---|---|---|
| None | None | None | None | None | None | None |
| Source | Motif | Strand | Matched sequence | Ref | Alt | Motif logo |
Conservation
PhyP scores of 46 vertebrates and 33 mammals across the +/-10bp region surrounding the SNP