Variant report

Variant	rs1815041
Chromosome Location	chr4:56245482-56245483
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	SMC3	chr4:56245335-56245603	Hela-S3	cervix:	n/a	n/a
8	FOS	chr4:56244874-56245640	MCF10A-Er-Src	breast:	n/a	n/a
9	STAT3	chr4:56245349-56245729	Hela-S3	cervix:	n/a	n/a
10	MYC	chr4:56245367-56245567	MCF10A-Er-Src	breast:	n/a	n/a
11	FOXA1	chr4:56245247-56245839	T-47D	breast:	n/a	n/a
12	FOXA2	chr4:56245351-56245594	A549	lung:	n/a	n/a
13	ZNF217	chr4:56245224-56245508	MCF-7	breast:	n/a	n/a
14	FOXP2	chr4:56245344-56245573	SK-N-MC	brain:	n/a	n/a
15	RFX5	chr4:56245134-56245689	Hela-S3	cervix:	n/a	n/a
16	GATA3	chr4:56245300-56245763	T-47D	breast:	n/a	chr4:56245700-56245721 chr4:56245707-56245716
17	RAD21	chr4:56245343-56245641	Hela-S3	cervix:	n/a	n/a
18	GATA3	chr4:56245318-56245801	MCF-7	breast:	n/a	chr4:56245700-56245721 chr4:56245707-56245716
19	NFYB	chr4:56245124-56245526	Hela-S3	cervix:	n/a	n/a
20	FOS	chr4:56245330-56245601	MCF10A-Er-Src	breast:	n/a	n/a
21	FOS	chr4:56245322-56245546	MCF10A-Er-Src	breast:	n/a	n/a
22	GATA3	chr4:56245320-56245717	T-47D	breast:	n/a	chr4:56245707-56245716
23	FOXA1	chr4:56245353-56245689	T-47D	breast:	n/a	n/a
24	STAT3	chr4:56245271-56245601	MCF10A-Er-Src	breast:	n/a	n/a
25	EP300	chr4:56245321-56245667	Hela-S3	cervix:	n/a	n/a
26	NFYA	chr4:56245346-56245556	Hela-S3	cervix:	n/a	n/a
27	CEBPB	chr4:56245221-56245757	Hela-S3	cervix:	n/a	n/a
28	STAT3	chr4:56245351-56245732	MCF10A-Er-Src	breast:	n/a	n/a
29	GATA3	chr4:56245356-56245582	MCF-7	breast:	n/a	n/a
30	RCOR1	chr4:56245200-56245601	Hela-S3	cervix:	n/a	n/a
31	MYC	chr4:56245270-56245684	MCF10A-Er-Src	breast:	n/a	n/a
32	STAT1	chr4:56245226-56245668	Hela-S3	cervix:	n/a	n/a
33	MAFK	chr4:56245339-56245776	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr4:56245103-56245515	Hela-S3	cervix:	n/a	n/a
35	STAT3	chr4:56245343-56245543	MCF10A-Er-Src	breast:	n/a	n/a
36	SIN3AK20	chr4:56245114-56245920	MCF-7	breast:	n/a	n/a
37	TFAP2A	chr4:56245208-56245739	Hela-S3	cervix:	n/a	n/a
38	BRCA1	chr4:56244781-56245639	Hela-S3	cervix:	n/a	n/a
39	EP300	chr4:56245352-56245814	T-47D	breast:	n/a	n/a
40	MAX	chr4:56245155-56245579	Hela-S3	cervix:	n/a	n/a
41	USF2	chr4:56245140-56245522	Hela-S3	cervix:	n/a	n/a
42	TCF7L2	chr4:56245191-56245594	Hela-S3	cervix:	n/a	n/a
43	STAT3	chr4:56245323-56245594	MCF10A-Er-Src	breast:	n/a	n/a
44	SP1	chr4:56245213-56245617	A549	lung:	n/a	n/a
45	TFAP2C	chr4:56245208-56245676	Hela-S3	cervix:	n/a	n/a

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

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

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1552523	1.00[AMR][1000 genomes]
rs17085690	1.00[AMR][1000 genomes]
rs17085747	1.00[AMR][1000 genomes]
rs17085816	1.00[AMR][1000 genomes]
rs17085850	1.00[AMR][1000 genomes]
rs1969380	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73819627	1.00[AMR][1000 genomes]
rs73819644	1.00[AMR][1000 genomes]
rs931395	1.00[AMR][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	chr4:56228400-56251000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr4:56232000-56247600	Weak transcription	Spleen	Spleen
5	chr4:56233200-56261600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:56235800-56247600	Weak transcription	Aorta	Aorta
7	chr4:56236400-56248400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr4:56237000-56247800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr4:56237200-56247800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr4:56239800-56251400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:56240200-56249400	Weak transcription	Left Ventricle	heart
12	chr4:56240400-56259600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr4:56240800-56247400	Weak transcription	Brain Angular Gyrus	brain
14	chr4:56243800-56247600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr4:56244000-56247800	Weak transcription	Brain Anterior Caudate	brain
16	chr4:56244200-56247400	Weak transcription	Brain Hippocampus Middle	brain
17	chr4:56244200-56247600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr4:56244800-56245600	Flanking Active TSS	Duodenum Mucosa	Duodenum
19	chr4:56244800-56246000	Enhancers	HMEC	breast
20	chr4:56244800-56246200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr4:56245000-56245600	Enhancers	Muscle Satellite Cultured Cells	--
22	chr4:56245000-56245600	Enhancers	HSMMtube	muscle
23	chr4:56245000-56246000	Flanking Active TSS	A549	lung
24	chr4:56245200-56245600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr4:56245200-56245600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:56245200-56245600	Active TSS	Hela-S3	cervix
27	chr4:56245200-56245600	Flanking Active TSS	NHEK	skin
28	chr4:56245200-56245800	Enhancers	Fetal Intestine Small	intestine
29	chr4:56245200-56245800	Enhancers	NHDF-Ad	bronchial
30	chr4:56245200-56245800	Enhancers	Osteobl	bone
31	chr4:56245200-56247400	Weak transcription	Brain Substantia Nigra	brain
32	chr4:56245400-56245800	Enhancers	Stomach Mucosa	stomach
33	chr4:56245400-56246000	Enhancers	K562	blood
34	chr4:56245400-56246200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr4:56245400-56246200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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