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Alteration chr1:27113734T>C

Likely effect

functional region (much evidence)


Model: extratranscriptic, Score: 97.41

direct link to this output 		     
Summary
  • Histone modifications in 3+ cell lines
  • Open Chromatin in 3+ cell lines
  • Polymerase in 3+ cell lines
  • Transcription Factor in 3+ cell lines
  • might affect genomic interactions
  • within TFBS
  • within active promoter of PIGV
analysed issue analysis result
alteration (phys. location) chr1:27113734T>C   IGV
alteration type SNV
alteration region extratranscriptic
known variant
Allele 'C' was not found in ExAC or 1000G.
promoters
RegulationSpotter - near TSSs of Ensembl transcripts
positionevidencegenetranscript
1: 27113463-27114013 DNase1H3K4me3PIGVENST00000430292
enhancers none found
epigenetic marks (RegulationSpotter)
DNase11:27113159-27114937
H3K4me31:27112668-27115956
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
H2AK5acIMR90
H2AZGM12878
K562
H2BK120acIMR90
H2BK12acIMR90
H3K14acIMR90
H3K18acIMR90
H3K23acIMR90
H3K27acGM12878
K562
Monocytes-CD14+ (PB) Roadmap
neutrophil myelocyte (BM)
T cells (PB) Roadmap		 Aorta EPC (VB)
HUVEC prol (CB)		 B cells (PB) Roadmap
DND-41
EM CD8+ ab T cell (VB)
Fetal Thymus
M0 macrophage (CB)
M0 macrophage (VB)
M2 macrophage (CB)
Monocytes-CD14+
Natural Killer cells (PB)		 H1ESC Fetal Adrenal Gland H1-neuronal progenitor H1-mesenchymal
IMR90
NHDF-AD
NHLF		 Osteobl Fetal Muscle Leg
Fetal Muscle Trunk
HSMM
HSMMtube
Psoas Muscle		 NHEK NH-A A549 Left Ventricle
Right Atrium		 HMEC Fetal Intestine Large
Fetal Intestine Small
Fetal Stomach
Gastric
Small Intestine		 HepG2 Spleen Placenta HeLa-S3
H3K36me3neutrophil myelocyte (BM) Fetal Intestine Small
H3K4acIMR90
H3K4me1eosinophil (VB)
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)
T cells (PB) Roadmap		 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 (CB)
CD4+ ab T cell (VB)
CD8+ ab T cell (CB)
CD8+ ab T cell (VB)
CM CD4+ ab T cell (VB)
DND-41
Fetal Thymus
M0 macrophage (VB)
M1 macrophage (CB)
M1 macrophage (VB)
M2 macrophage (CB)
M2 macrophage (VB)
Monocytes-CD14+
Natural Killer cells (PB)
Thymus		 H9 iPS DF 19.11
iPS-20b		 Fetal Adrenal Gland IMR90
NHDF-AD
NHLF		 Osteobl Fetal Muscle Leg
Fetal Muscle Trunk
HSMM
HSMMtube
Psoas Muscle		 NHEK NH-A A549 HMEC Fetal Intestine Large
Fetal Intestine Small
Fetal Stomach		 HepG2 H1-trophoblast
Placenta		 HeLa-S3
H3K4me2GM12878
K562		 HUVEC DND-41
Monocytes-CD14+		 H1ESC IMR90
NHDF-AD		 Osteobl HSMM
HSMMtube		 NHEK NH-A A549 HMEC HepG2 HeLa-S3
H3K4me3GM12878
K562
Monocytes-CD14+ (PB) Roadmap
naive B cell (To)
T cells (PB) Roadmap		 Aorta B cells (PB) Roadmap
CD14+CD16- monocyte (VB)
DND-41
Fetal Thymus
Monocytes-CD14+
Natural Killer cells (PB)
Thymus		 H1ESC iPS-20b Fetal Adrenal Gland IMR90
NHDF-AD
NHLF		 Osteobl Fetal Muscle Leg
Fetal Muscle Trunk
HSMM
HSMMtube
Psoas Muscle		 NH-A A549 Left Ventricle
Right Atrium		 Fetal Intestine Large
Fetal Intestine Small
Fetal Stomach		 HepG2 HeLa-S3
H3K56acIMR90
H3K79me2GM12878
K562
H3K9acGM12878
K562		 HUVEC DND-41
Monocytes-CD14+		 H1ESC iPS-20b IMR90
NHDF-AD
NHLF		 HSMM
HSMMtube		 NHEK NH-A A549 HMEC HepG2 HeLa-S3
H4K5acIMR90
H4K8acIMR90
H4K91acIMR90
show features in Ensembl  explain
polymerase
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
PolIIGM12878
K562		 H1ESC
show features in Ensembl  explain
open chromatin
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
DNase1GM12878
K562		 CD14+CD16- monocyte (CB)
CD8+ ab T cell (CB)
M2 macrophage (VB)		 H1ESC IMR90
NHDF-AD
NHLF		 HSMM
HSMMtube		 NH-A
show features in Ensembl  explain
TFBS (confirmed)
bound TFBSblood 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
BCL3GM12878
BCLAF1GM12878
ELF1GM12878
Egr1K562
HEY1K562 HepG2
NFKBGM12891
GM18505
GM18951
GM19099
POU2F2GM12878
GM12891
TAF1GM12891
K562		 H1ESC
THAP1K562
Yy1GM12878
GM12891
GM12892
K562		 SKNSHRA HCT116
show features in Ensembl  explain
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 symbolEnsembl IDshow transcripts

hide
PIGV ENSG00000060642
protein-coding:
ENST00000430292
promoterCD34
GM12878
HCC1954
K562		 HUVEC CD4 Memory
CD4 Naive
CD4 T
CD8 Naive		 H1 derived mesendoderm cell
H1ESC		 IPS19.11
IPS6.9		 H1 derived neural progenitors Foreskin fibroblast
H1 derived mesenchymal stem cell
IMR90
NHLF		 HSMM Foreskin keratinocyte
Foreskin melanocyte
NHEK		 Brain hippocampus middle HMEC
MCF7		 HCT116 HEP PANC H1 derived trophoblast HELA A549
ARID1A ENSG00000117713
protein-coding:
ENST00000324856
ENST00000374152
ENST00000430799
ENST00000457599
ENST00000524572
ENST00000540690
nonsense mediated decay:
ENST00000466382
ENST00000532781
retained intron:
ENST00000430291
distant element, interacts w/ promoterCD34
GM12878
K562		 HUVEC CD4 T IPS19.11
IPS6.9		 H1 derived neural progenitors Foreskin fibroblast
H1 derived mesenchymal stem cell
IMR90
NHLF		 HSMM Foreskin keratinocyte
Foreskin melanocyte
NHEK		 Brain hippocampus middle HMEC
MCF7		 HCT116 HEP H1 derived trophoblast HELA
CNKSR1 ENSG00000142675
processed transcript:
ENST00000528001
nonsense mediated decay:
ENST00000528281
retained intron:
ENST00000524529
ENST00000531150
distant element, interacts w/ promoterForeskin keratinocyte
CRYBG2 ENSG00000176092
retained intron:
ENST00000520372
processed transcript:
ENST00000522923
distant element, interacts w/ promoterK562 H1ESC NHEK
ENSG00000225891
antisense:
ENST00000423060
distant element, interacts w/ promoterIMR90
ENSG00000226698
antisense:
ENST00000448791
distant element, interacts w/ promoterIMR90
ENSG00000229247
processed pseudogene:
ENST00000428860
distant element, interacts w/ promoterIMR90
ENSG00000235069
processed pseudogene:
ENST00000443847
distant element, interacts w/ promoterIMR90
ENSG00000236782
antisense:
ENST00000407889
ENST00000414762
ENST00000433939
ENST00000444682
distant element, interacts w/ promoterCD34
K562		 CD8 Naive H1 derived mesendoderm cell IPS6.9 Foreskin fibroblast
H1 derived mesenchymal stem cell
IMR90
NHLF		 HSMM Foreskin keratinocyte
Foreskin melanocyte
NHEK		 Brain hippocampus middle HMEC HCT116 HEP PANC HELA
ENSG00000238316
snoRNA:
ENST00000459201
distant element, interacts w/ promoterIMR90
ENSG00000241188
misc RNA:
ENST00000477476
distant element, interacts w/ promoterGM12878 IMR90
ENSG00000243905
misc RNA:
ENST00000497096
distant element, interacts w/ promoterIMR90
ENSG00000252802
misc RNA:
ENST00000516993
distant element, interacts w/ promoterIMR90
ENSG00000266138
misc RNA:
ENST00000578818
distant element, interacts w/ promoterIMR90
GPATCH3 ENSG00000198746
protein-coding:
ENST00000361720
ENST00000445019
ENST00000450844
distant element, interacts w/ promoterHCC1954
K562		 H1 derived mesendoderm cell
H1ESC		 IPS19.11
IPS6.9		 Foreskin fibroblast
H1 derived mesenchymal stem cell
IMR90
NHLF		 HSMM Foreskin keratinocyte
Foreskin melanocyte
NHEK		 Brain hippocampus middle HMEC HCT116 HEP PANC H1 derived trophoblast HELA A549
GPN2 ENSG00000142751
protein-coding:
ENST00000374133
ENST00000374135
ENST00000431781
retained intron:
ENST00000477418
processed transcript:
ENST00000461282
distant element, interacts w/ promoterCD34
HCC1954
K562		 CD4 Memory
CD4 Naive
CD8 Naive		 H1 derived mesendoderm cell
H1ESC		 IPS19.11
IPS6.9		 Foreskin fibroblast
H1 derived mesenchymal stem cell
IMR90
NHLF		 Foreskin keratinocyte
Foreskin melanocyte
NHEK		 Brain hippocampus middle HMEC
MCF7		 PANC H1 derived trophoblast A549
GPR3 ENSG00000181773
protein-coding:
ENST00000374024
distant element, interacts w/ promoterK562 H1ESC IPS19.11 Foreskin fibroblast
IMR90
NHLF		 HSMM Foreskin keratinocyte
Foreskin melanocyte		 HMEC HCT116 HEP
HMGN2 ENSG00000198830
protein-coding:
ENST00000361427
processed transcript:
ENST00000460563
ENST00000463817
ENST00000464888
ENST00000466194
ENST00000467700
ENST00000468388
ENST00000479815
ENST00000493418
distant element, interacts w/ promoterIMR90
KDF1 ENSG00000175707
protein-coding:
ENST00000320567
distant element, interacts w/ promoterH1ESC IPS19.11
IPS6.9		 Foreskin fibroblast
IMR90		 Foreskin keratinocyte
Foreskin melanocyte
NHEK		 HMEC HCT116 HEP H1 derived trophoblast
LOC101928728 ENSG00000260063
antisense:
ENST00000569378
distant element, interacts w/ promoterK562 CD4 Memory
CD4 Naive		 IMR90 MCF7
MAP3K6 ENSG00000142733
protein-coding:
ENST00000357582
ENST00000374040
ENST00000493901
distant element, interacts w/ promoterH1 derived mesendoderm cell IPS19.11 Foreskin fibroblast
IMR90
NHLF		 HSMM Foreskin keratinocyte
Foreskin melanocyte		 HMEC HCT116 HEP HELA A549
MIR1976 ENSG00000238705
miRNA:
ENST00000459548
distant element, interacts w/ promoterIMR90
NR0B2 ENSG00000131910
protein-coding:
ENST00000254227
distant element, interacts w/ promoterIMR90
NUDC ENSG00000090273
protein-coding:
ENST00000321265
ENST00000435827
ENST00000452707
processed transcript:
ENST00000484772
distant element, interacts w/ promoterHCC1954
K562		 CD4 Memory
CD4 Naive
CD4 T		 H1 derived mesendoderm cell
H1ESC		 IPS19.11
IPS6.9		 Foreskin fibroblast
H1 derived mesenchymal stem cell
IMR90
NHLF		 HSMM Foreskin keratinocyte
Foreskin melanocyte
NHEK		 Brain hippocampus middle HCT116 HEP PANC H1 derived trophoblast HELA A549
PDIK1L ENSG00000175087
protein-coding:
ENST00000374269
ENST00000374271
ENST00000444713
distant element, interacts w/ promoterGM12878
PIGV ENSG00000060642
protein-coding:
ENST00000078527
ENST00000374145
ENST00000431541
ENST00000449950
ENST00000455364
nonsense mediated decay:
ENST00000472757
distant element, interacts w/ promoterCD34
GM12878
HCC1954
K562		 HUVEC CD4 Memory
CD4 Naive
CD4 T
CD8 Naive		 H1 derived mesendoderm cell
H1ESC		 IPS19.11
IPS6.9		 H1 derived neural progenitors Foreskin fibroblast
H1 derived mesenchymal stem cell
IMR90
NHLF		 HSMM Foreskin keratinocyte
Foreskin melanocyte
NHEK		 Brain hippocampus middle HMEC
MCF7		 HCT116 HEP PANC H1 derived trophoblast HELA A549
RPS6KA1 ENSG00000117676
protein-coding:
ENST00000374162
ENST00000374166
ENST00000374168
ENST00000403732
ENST00000438977
ENST00000526792
ENST00000529454
ENST00000530003
ENST00000531382
retained intron:
ENST00000474934
ENST00000524436
ENST00000525582
ENST00000527264
ENST00000530305
ENST00000530607
ENST00000531113
nonsense mediated decay:
ENST00000366866
ENST00000374163
ENST00000525525
ENST00000526040
processed transcript:
ENST00000488985
distant element, interacts w/ promoterK562 H1 derived mesendoderm cell
H1ESC		 IMR90 NHEK Brain hippocampus middle HCT116 HEP PANC HELA
SFN ENSG00000175793
protein-coding:
ENST00000339276
distant element, interacts w/ promoterGM12878 IMR90 Foreskin keratinocyte MCF7
SH3BGRL3 ENSG00000142669
protein-coding:
ENST00000270792
ENST00000319041
distant element, interacts w/ promoterCD4 Memory
CD4 T
SYTL1 ENSG00000142765
protein-coding:
ENST00000318074
ENST00000473280
retained intron:
ENST00000483926
ENST00000485269
ENST00000496001
distant element, interacts w/ promoterCD4 Memory HMEC
TRNP1 ENSG00000253368
protein-coding:
ENST00000522111
ENST00000531285
distant element, interacts w/ promoterH1ESC IPS19.11
IPS6.9		 Foreskin fibroblast
H1 derived mesenchymal stem cell
IMR90
NHLF		 Foreskin keratinocyte
Foreskin melanocyte
NHEK		 HMEC HCT116 HEP A549
UBXN11 ENSG00000158062
protein-coding:
ENST00000314675
ENST00000357089
ENST00000374215
ENST00000374221
ENST00000374223
ENST00000421827
ENST00000423664
ENST00000436301
ENST00000450041
ENST00000535108
retained intron:
ENST00000472155
ENST00000475591
ENST00000494942
distant element, interacts w/ promoterHCC1954
K562		 CD4 Memory
CD4 T		 H1 derived mesendoderm cell
H1ESC		 IPS19.11
IPS6.9		 Foreskin fibroblast
H1 derived mesenchymal stem cell
IMR90
NHLF		 Foreskin keratinocyte
Foreskin melanocyte
NHEK		 Brain hippocampus middle HMEC HEP PANC H1 derived trophoblast HELA A549
ZDHHC18 ENSG00000204160
protein-coding:
ENST00000374141
ENST00000374142
ENST00000488397
ENST00000534643
processed transcript:
ENST00000478902
distant element, interacts w/ promoterK562 Foreskin fibroblast
H1 derived mesenchymal stem cell
IMR90
NHLF		 HSMM Foreskin melanocyte
NHEK		 HMEC HELA A549
ZNF593 ENSG00000142684
protein-coding:
ENST00000270812
ENST00000374266
distant element, interacts w/ promoterCD34
GM12878
K562		 CD8 Naive H1 derived mesendoderm cell IPS6.9 Foreskin fibroblast
H1 derived mesenchymal stem cell
IMR90
NHLF		 HSMM Foreskin keratinocyte
Foreskin melanocyte
NHEK		 Brain hippocampus middle HMEC HCT116 HEP PANC HELA

show interactions as plot
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3770.949
1.1540.962
(flanking)2.0960.962
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
CADD (scaled) 12.8   (please see documentation for details)
chromosome 1
strand 1
original chrDNA sequence snippet AAACTGGCCGCTCCCCCCAATAGACGGTTTTGTTGAGTTCG
altered chrDNA sequence snippet AAACTGGCCGCTCCCCCCAACAGACGGTTTTGTTGAGTTCG
speed 0.53 s

All positions are in basepairs (bp) if not explicitly stated differently.
Abbreviations: aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
show score composition
mod_perl version: CGI