Variant report

Variant	rs73238603
Chromosome Location	chr4:47564441-47564442
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:47564293-47564746	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr4:47564249-47564849	SH-SY5Y	brain:	n/a	n/a
3	GATA3	chr4:47563962-47564935	SK-N-SH	brain:	n/a	n/a
4	EP300	chr4:47564104-47564774	SK-N-SH	brain:	n/a	n/a
5	TEAD4	chr4:47564203-47564912	SK-N-SH	brain:	n/a	n/a
6	NFIC	chr4:47564200-47564827	SK-N-SH	brain:	n/a	n/a
7	GATA3	chr4:47564090-47564834	SK-N-SH	brain:	n/a	n/a
8	GATA2	chr4:47564278-47564708	SH-SY5Y	brain:	n/a	n/a
9	EP300	chr4:47564343-47564641	SK-N-SH_RA	brain:	n/a	n/a
10	EP300	chr4:47564029-47564946	SK-N-SH	brain:	n/a	n/a
11	EP300	chr4:47564314-47564638	SK-N-SH_RA	brain:	n/a	n/a
12	TEAD4	chr4:47564272-47564673	SK-N-SH	brain:	n/a	n/a
13	TCF12	chr4:47564143-47564867	SK-N-SH	brain:	n/a	n/a
14	PBX3	chr4:47564233-47564762	SK-N-SH	brain:	n/a	n/a
15	EP300	chr4:47564249-47564822	SK-N-SH	brain:	n/a	n/a
16	RXRA	chr4:47564315-47564697	SK-N-SH	brain:	n/a	n/a
17	TCF12	chr4:47564134-47564894	SK-N-SH	brain:	n/a	n/a
18	PBX3	chr4:47564177-47564786	SK-N-SH	brain:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:47562873..47564467-chr4:47565898..47568483,2	K562	blood:
2	chr4:47559378..47560960-chr4:47564050..47565557,2	K562	blood:
3	chr4:47464391..47466758-chr4:47562914..47565162,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000248254	TF binding region
ENSG00000169019	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10004038	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11934428	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11947712	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28488258	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28509198	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34208443	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4362797	0.83[ASN][1000 genomes]
rs4599383	0.83[ASN][1000 genomes]
rs6837171	0.83[ASN][1000 genomes]
rs73237094	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237095	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237098	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237099	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237100	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237101	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237102	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238604	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238607	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73238608	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829923	chr4:47436139-47678443	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1008515	chr4:47488431-47906835	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv948568	chr4:47488431-47907524	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1004939	chr4:47488573-47901460	Bivalent Enhancer Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv537080	chr4:47488573-47901460	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv997471	chr4:47489412-47895223	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv998892	chr4:47493552-47863354	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv537081	chr4:47493552-47863354	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv1000337	chr4:47493907-47902019	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv594118	chr4:47560386-47917730	Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47512400-47577200	Weak transcription	Small Intestine	intestine
2	chr4:47534600-47580800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:47534600-47592000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr4:47536200-47571000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr4:47538600-47566800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr4:47538800-47571000	Weak transcription	Brain Hippocampus Middle	brain
7	chr4:47539600-47589000	Weak transcription	Colonic Mucosa	Colon
8	chr4:47541000-47571000	Weak transcription	Spleen	Spleen
9	chr4:47544800-47574000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:47545400-47566800	Strong transcription	Placenta	Placenta
11	chr4:47546400-47589400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr4:47548800-47583800	Weak transcription	Psoas Muscle	Psoas
13	chr4:47549000-47574000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr4:47549400-47566800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:47549400-47570800	Weak transcription	Esophagus	oesophagus
16	chr4:47549400-47570800	Weak transcription	NHLF	lung
17	chr4:47549400-47573600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr4:47549400-47574800	Weak transcription	Primary T cells from cord blood	blood
19	chr4:47549400-47576800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr4:47549600-47570800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr4:47550800-47566800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr4:47553000-47570800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr4:47554000-47566800	Weak transcription	NHDF-Ad	bronchial
24	chr4:47554200-47566200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:47555800-47594800	Weak transcription	Stomach Mucosa	stomach
26	chr4:47556000-47570800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr4:47556200-47570200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:47556400-47578800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr4:47556400-47588000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr4:47559400-47566000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:47559600-47565200	Strong transcription	Primary B cells from peripheral blood	blood
32	chr4:47559600-47567200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:47559800-47564600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr4:47559800-47565800	Strong transcription	Adipose Nuclei	Adipose
35	chr4:47560000-47570800	Weak transcription	Gastric	stomach
36	chr4:47560200-47565600	Strong transcription	HSMM	muscle
37	chr4:47560200-47566800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr4:47560200-47570800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr4:47560200-47571000	Weak transcription	Brain Angular Gyrus	brain
40	chr4:47560200-47574600	Weak transcription	Fetal Intestine Small	intestine
41	chr4:47560200-47579400	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr4:47560400-47570800	Weak transcription	Fetal Stomach	stomach
43	chr4:47560400-47573800	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr4:47560600-47566200	Weak transcription	HUVEC	blood vessel
45	chr4:47560600-47566600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr4:47560600-47567200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr4:47560600-47570800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr4:47560600-47573600	Weak transcription	Pancreas	Pancrea
49	chr4:47560800-47570400	Weak transcription	Colon Smooth Muscle	Colon
50	chr4:47561000-47570000	Weak transcription	Stomach Smooth Muscle	stomach

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