Variant report

Variant	rs28448391
Chromosome Location	chr4:144263142-144263143
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr4:144263067-144263430	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:144261573..144263488-chr4:144322361..144324414,2	K562	blood:
2	chr4:144254658..144259448-chr4:144261105..144264742,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178972	TF binding region
MIR3139	TF binding region
ENSG00000178972	Chromatin interaction
ENSG00000109458	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17017563	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17017629	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17017662	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28377860	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28676298	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28680635	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6825973	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72947118	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033902	chr4:144114413-144285772	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1026110	chr4:144239825-144292148	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:144259200-144264000	Weak transcription	Small Intestine	intestine
2	chr4:144259200-144272400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:144259400-144265400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:144259400-144268600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr4:144259400-144272000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:144259400-144272600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr4:144259600-144264200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr4:144259600-144264200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr4:144259600-144264600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:144259600-144265000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr4:144259600-144276200	Weak transcription	Fetal Kidney	kidney
12	chr4:144259800-144264200	Weak transcription	HMEC	breast
13	chr4:144259800-144264600	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr4:144259800-144264800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:144259800-144264800	Weak transcription	Fetal Brain Female	brain
16	chr4:144259800-144265400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:144259800-144268600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr4:144260000-144264400	Weak transcription	NHEK	skin
19	chr4:144260000-144267400	Weak transcription	Stomach Mucosa	stomach
20	chr4:144260000-144268600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr4:144260000-144272800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:144260200-144264200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:144260200-144264600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:144260200-144268600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr4:144261000-144264200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:144261000-144264600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr4:144261000-144264600	Weak transcription	NHLF	lung
28	chr4:144261000-144265200	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr4:144261000-144265600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr4:144261000-144266000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr4:144261000-144268600	Weak transcription	Primary B cells from cord blood	blood
32	chr4:144261200-144263200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:144261400-144264200	Weak transcription	Liver	Liver
34	chr4:144261400-144264400	Weak transcription	Fetal Stomach	stomach
35	chr4:144261400-144265400	Weak transcription	HepG2	liver
36	chr4:144261600-144272600	Weak transcription	Adipose Nuclei	Adipose
37	chr4:144262000-144263200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr4:144262000-144263200	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr4:144262000-144263400	Flanking Active TSS	Brain Hippocampus Middle	brain
40	chr4:144262200-144263600	Flanking Active TSS	Fetal Heart	heart
41	chr4:144262400-144263200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr4:144262400-144263200	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr4:144262400-144263200	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr4:144262400-144263200	Enhancers	K562	blood
45	chr4:144262400-144263400	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr4:144262400-144263400	Enhancers	Placenta Amnion	Placenta Amnion
47	chr4:144262400-144263600	Enhancers	Brain Cingulate Gyrus	brain
48	chr4:144262400-144263600	Enhancers	Rectal Smooth Muscle	rectum
49	chr4:144262400-144265400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr4:144262600-144263200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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