Likely effect |
non-functional region (much evidence)
Model: extratranscriptic, Score: 11.16
direct link to this output
|
|
| Summary |
- Histone modifications in 3+ cell lines
- might affect genomic interactions
|
| analysed issue |
analysis result |
| alteration (phys. location) | chr4:89442139T>G IGV
|
| alteration type | SNV |
| alteration region | extratranscriptic |
| known variant |
| database | homozygous (G/G) | heterozygous | allele carriers |
| 1000G |
0 | 1 | 1 |
| ExAC | - | - | - |
|
| promoters | | RegulationSpotter - near TSSs of Ensembl transcripts |
| position | evidence | gene | transcript | | 4: 89441699-89442249 |
no histone marks | HERC3 | ENST00000601319 |
|
| enhancers | none found |
| epigenetic marks (RegulationSpotter) | no regulatory regions annotated |
| histone modifications | genomic
feature | blood |
artery |
vein |
immune |
ESC |
iPSC |
endocrin |
neural |
conn.tiss. |
bone |
muscle |
skin |
brain |
eye |
lung |
heart |
breast |
GIT |
liver |
pancreas |
spleen |
kidney |
ovary |
placenta |
amnion |
cervix |
testis |
| H3K36me3 | erythroblast (CB)
GM12878
K562
Monocytes-CD14+ (PB) Roadmap
MSC (VB)
naive B cell (To)
naive B cell (VB)
neutrophil (CB)
neutrophil (VB)
neutrophil myelocyte (BM) |
| EPC (VB)
HUVEC
HUVEC prol (CB) |
B cells (PB) Roadmap
CD14+CD16- monocyte (CB)
CD14+CD16- monocyte (VB)
CD38- naive B cell (CB)
CD4+ ab T cell (VB)
CD8+ ab T cell (CB)
CM CD4+ ab T cell (VB)
DND-41
EM CD8+ ab T cell (VB)
Fetal Thymus
M0 macrophage (CB)
M0 macrophage (VB)
M1 macrophage (CB)
M1 macrophage (VB)
M2 macrophage (CB)
M2 macrophage (VB)
Monocytes-CD14+
Natural Killer cells (PB) |
| iPS-20b |
| | | Osteobl |
Fetal Muscle Leg
HSMM
HSMMtube |
NHEK |
NH-A |
| A549 |
| HMEC |
Fetal Intestine Large |
HepG2 |
| | | | Placenta |
| | |
| H3K4me1 | GM12878 |
| | DND-41 |
| | | | | | | | | | | | | | | | | | | | | | |
| H3K79me2 | GM12878
K562 |
| | | | | | | | | HSMM
HSMMtube |
| | | | | | | | | | | | | | | |
| H4K20me1 | | | | | | | | | | | | | | | | | | | | | | | | | | HeLa-S3 |
|
show features in Ensembl
explain |
| polymerase | none found |
| open chromatin | none found |
| TFBS (confirmed) | none found |
| TFBS (by motif) | no TFBS-like motif annotated
|
| genomic interactions | HiC interactions
| associated gene(s) |
interacting element harbouring variant... |
blood |
vein |
immune |
ESC |
iPSC |
endocrin |
neural |
conn.tiss. |
bone |
muscle |
skin |
brain |
breast |
GIT |
liver |
pancreas |
kidney |
placenta |
cervix |
testis |
lung |
| gene symbol | Ensembl ID | show transcripts | | HERC3 | ENSG00000138641 | | promoter | GM12878 |
HUVEC |
CD4 Naive
CD4 T |
| IPS6.9 |
| | Foreskin fibroblast
IMR90
NHLF |
| HSMM |
Foreskin keratinocyte
NHEK |
| HMEC |
| | | | | | | |
| ENSG00000252322 | | distant element, interacts w/ promoter | GM12878 |
HUVEC |
| | | | | | | | | | | | | | | | | | |
| FAM13A | ENSG00000138640 | | distant element, interacts w/ promoter | | | | | | | | | | HSMM |
| | | | | | | | | | |
| HERC3 | ENSG00000138641 | | distant element, interacts w/ promoter | GM12878 |
HUVEC |
| | IPS6.9 |
| | IMR90 |
| | NHEK |
| | | | | | | | | |
| LOC100129137 | ENSG00000249755 | | distant element, interacts w/ promoter | GM12878 |
| | | | | | | | | | | | | | | | | | | |
| PIGY | ENSG00000255072 | | distant element, interacts w/ promoter | GM12878 |
HUVEC |
CD4 Naive
CD4 T |
| IPS6.9 |
| | Foreskin fibroblast
IMR90
NHLF |
| HSMM |
Foreskin keratinocyte
NHEK |
| HMEC |
| | | | | | | |
show interactions as plot
|
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 0.092 | 0 | | -0.757 | 0 | | (flanking) | -3.409 | 0 |
explain score(s)
and/or inspect your position(s) in in UCSC Genome Browser |
| CADD (scaled) | 7.02 (please see documentation for details) |
| chromosome | 4 |
| strand | 1 |
| original chrDNA sequence snippet | CCAAACAAACAAACGACTACTGCAAACTGGTTTATTTTTTA |
| altered chrDNA sequence snippet | CCAAACAAACAAACGACTACGGCAAACTGGTTTATTTTTTA |
| speed | 0.45 s |
