Variant report

Variant	rs1961107
Chromosome Location	chr4:56245333-56245334
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	TBP	chr4:56245048-56245552	Hela-S3	cervix:	n/a	n/a
2	FOS	chr4:56245276-56245641	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr4:56245127-56245534	MCF10A-Er-Src	breast:	n/a	n/a
4	GATA3	chr4:56245194-56245829	MCF-7	breast:	n/a	chr4:56245700-56245721 chr4:56245707-56245716
5	FOXA2	chr4:56245215-56245571	A549	lung:	n/a	n/a
6	CHD2	chr4:56245233-56245707	Hela-S3	cervix:	n/a	n/a
7	FOS	chr4:56244874-56245640	MCF10A-Er-Src	breast:	n/a	n/a
8	FOXA1	chr4:56245247-56245839	T-47D	breast:	n/a	n/a
9	ZNF217	chr4:56245224-56245508	MCF-7	breast:	n/a	n/a
10	RFX5	chr4:56245134-56245689	Hela-S3	cervix:	n/a	n/a
11	GATA3	chr4:56245300-56245763	T-47D	breast:	n/a	chr4:56245700-56245721 chr4:56245707-56245716
12	GATA3	chr4:56245318-56245801	MCF-7	breast:	n/a	chr4:56245700-56245721 chr4:56245707-56245716
13	NFYB	chr4:56245124-56245526	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr4:56245178-56245426	Hela-S3	cervix:	n/a	n/a
15	FOS	chr4:56245330-56245601	MCF10A-Er-Src	breast:	n/a	n/a
16	FOS	chr4:56245322-56245546	MCF10A-Er-Src	breast:	n/a	n/a
17	GATA3	chr4:56245320-56245717	T-47D	breast:	n/a	chr4:56245707-56245716
18	STAT3	chr4:56245271-56245601	MCF10A-Er-Src	breast:	n/a	n/a
19	EP300	chr4:56245321-56245667	Hela-S3	cervix:	n/a	n/a
20	CEBPB	chr4:56245221-56245757	Hela-S3	cervix:	n/a	n/a
21	RCOR1	chr4:56245200-56245601	Hela-S3	cervix:	n/a	n/a
22	MYC	chr4:56245270-56245684	MCF10A-Er-Src	breast:	n/a	n/a
23	STAT1	chr4:56245226-56245668	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr4:56245103-56245515	Hela-S3	cervix:	n/a	n/a
25	SIN3AK20	chr4:56245114-56245920	MCF-7	breast:	n/a	n/a
26	TFAP2A	chr4:56245208-56245739	Hela-S3	cervix:	n/a	n/a
27	BRCA1	chr4:56244781-56245639	Hela-S3	cervix:	n/a	n/a
28	MAX	chr4:56245155-56245579	Hela-S3	cervix:	n/a	n/a
29	USF2	chr4:56245140-56245522	Hela-S3	cervix:	n/a	n/a
30	TCF7L2	chr4:56245191-56245594	Hela-S3	cervix:	n/a	n/a
31	STAT3	chr4:56245323-56245594	MCF10A-Er-Src	breast:	n/a	n/a
32	SP1	chr4:56245213-56245617	A549	lung:	n/a	n/a
33	TFAP2C	chr4:56245208-56245676	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:56236823..56239564-chr4:56243563..56245351,2	MCF-7	breast:
2	chr4:56212360..56213215-chr4:56245086..56246127,4	MCF-7	breast:
3	chr4:56240281..56248484-chr4:56258541..56264383,10	MCF-7	breast:
4	chr4:56243121..56245532-chr4:56269359..56271036,2	MCF-7	breast:
5	chr4:56243246..56246194-chr4:56252558..56255228,2	K562	blood:
6	chr4:56245158..56247160-chr4:56262133..56263862,2	K562	blood:
7	chr4:56232345..56235244-chr4:56243502..56246293,2	MCF-7	breast:
8	chr4:56240192..56241907-chr4:56242608..56245605,4	K562	blood:

Variant related genes	Relation type
SRD5A3-AS1	TF binding region
ENSG00000273257	Chromatin interaction
ENSG00000134851	Chromatin interaction
ENSG00000128039	Chromatin interaction
ENSG00000249700	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10010762	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10021233	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10024928	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1818460	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1818461	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2538	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28609134	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4089487	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs475465	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs476184	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs525271	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs552792	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs552950	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs556072	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs573960	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs576732	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58506276	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62305200	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs819203	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs819266	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs819267	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs819268	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs819269	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs819270	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56213800-56251400	Weak transcription	Pancreas	Pancrea
2	chr4:56214400-56247600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:56228400-56245400	Weak transcription	K562	blood
4	chr4:56228400-56251000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr4:56232000-56247600	Weak transcription	Spleen	Spleen
6	chr4:56233200-56261600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:56235800-56247600	Weak transcription	Aorta	Aorta
8	chr4:56236400-56248400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr4:56237000-56245400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:56237000-56247800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:56237200-56247800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr4:56239800-56251400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:56240200-56249400	Weak transcription	Left Ventricle	heart
14	chr4:56240400-56259600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr4:56240800-56247400	Weak transcription	Brain Angular Gyrus	brain
16	chr4:56243800-56247600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr4:56244000-56247800	Weak transcription	Brain Anterior Caudate	brain
18	chr4:56244200-56247400	Weak transcription	Brain Hippocampus Middle	brain
19	chr4:56244200-56247600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr4:56244800-56245600	Flanking Active TSS	Duodenum Mucosa	Duodenum
21	chr4:56244800-56246000	Enhancers	HMEC	breast
22	chr4:56244800-56246200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:56245000-56245400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:56245000-56245400	Active TSS	Stomach Mucosa	stomach
25	chr4:56245000-56245600	Enhancers	Muscle Satellite Cultured Cells	--
26	chr4:56245000-56245600	Enhancers	HSMMtube	muscle
27	chr4:56245000-56246000	Flanking Active TSS	A549	lung
28	chr4:56245200-56245600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr4:56245200-56245600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr4:56245200-56245600	Active TSS	Hela-S3	cervix
31	chr4:56245200-56245600	Flanking Active TSS	NHEK	skin
32	chr4:56245200-56245800	Enhancers	Fetal Intestine Small	intestine
33	chr4:56245200-56245800	Enhancers	NHDF-Ad	bronchial
34	chr4:56245200-56245800	Enhancers	Osteobl	bone
35	chr4:56245200-56247400	Weak transcription	Brain Substantia Nigra	brain

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