Variant report

Variant	rs852480
Chromosome Location	chr7:5638496-5638497
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	POLR2A	chr7:5638379-5638781	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr7:5637938-5638884	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr7:5638163-5638881	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr7:5637211-5639498	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr7:5637557-5638908	Hela-S3	cervix:	n/a	n/a
6	WRNIP1	chr7:5638022-5638583	GM12878	blood:	n/a	n/a
7	EGR1	chr7:5638419-5638706	GM12878	blood:	n/a	chr7:5638561-5638576 chr7:5638562-5638575 chr7:5638635-5638648 chr7:5638563-5638577 chr7:5638558-5638580 chr7:5638562-5638575
8	POLR2A	chr7:5637379-5639819	GM12892	blood:	n/a	n/a
9	TRIM28	chr7:5638301-5638825	K562	blood:	n/a	n/a
10	NFATC1	chr7:5638265-5638546	GM12878	blood:	n/a	n/a
11	CEBPB	chr7:5638360-5638723	K562	blood:	n/a	n/a
12	EGR1	chr7:5638190-5638774	K562	blood:	n/a	chr7:5638561-5638576 chr7:5638562-5638575 chr7:5638635-5638648 chr7:5638563-5638577 chr7:5638558-5638580 chr7:5638562-5638575
13	USF1	chr7:5638334-5638761	K562	blood:	n/a	n/a
14	SIN3AK20	chr7:5638157-5638896	PANC-1	pancreas:	n/a	n/a
15	EGR1	chr7:5638234-5639117	K562	blood:	n/a	chr7:5638561-5638576 chr7:5638562-5638575 chr7:5638635-5638648 chr7:5638563-5638577 chr7:5638558-5638580 chr7:5638562-5638575
16	POLR2A	chr7:5637526-5639628	GM12878	blood:	n/a	n/a
17	STAT5A	chr7:5638376-5638678	GM12878	blood:	n/a	n/a
18	MYC	chr7:5637575-5639059	K562	blood:	n/a	chr7:5638083-5638092 chr7:5638091-5638100
19	POLR2A	chr7:5638448-5638846	H1-hESC	embryonic stem cell:	n/a	n/a
20	TCF12	chr7:5638362-5638950	ECC-1	luminal epithelium:	n/a	chr7:5638613-5638623
21	SIN3A	chr7:5638459-5638673	H1-hESC	embryonic stem cell:	n/a	chr7:5638580-5638591
22	MAX	chr7:5638347-5638954	A549	lung:	n/a	n/a
23	RAD21	chr7:5638361-5638720	K562	blood:	n/a	chr7:5638395-5638409
24	TAL1	chr7:5638443-5638838	K562	blood:	n/a	chr7:5638473-5638488
25	PML	chr7:5638024-5638822	K562	blood:	n/a	n/a
26	RUNX3	chr7:5638344-5638834	GM12878	blood:	n/a	n/a
27	POLR2A	chr7:5637304-5639803	K562	blood:	n/a	n/a
28	CHD2	chr7:5638469-5638828	Hela-S3	cervix:	n/a	n/a
29	FOXM1	chr7:5638318-5638616	GM12878	blood:	n/a	n/a
30	ELF1	chr7:5638370-5638880	K562	blood:	n/a	n/a
31	NFIC	chr7:5638344-5638700	GM12878	blood:	n/a	n/a
32	EP300	chr7:5638061-5638959	K562	blood:	n/a	n/a
33	POLR2A	chr7:5638171-5639152	K562	blood:	n/a	n/a
34	CBX3	chr7:5637879-5638923	K562	blood:	n/a	n/a
35	EGR1	chr7:5638337-5638858	ECC-1	luminal epithelium:	n/a	chr7:5638561-5638576 chr7:5638562-5638575 chr7:5638635-5638648 chr7:5638563-5638577 chr7:5638558-5638580 chr7:5638562-5638575
36	GABPA	chr7:5638341-5639059	K562	blood:	n/a	n/a
37	MAX	chr7:5637719-5639153	K562	blood:	n/a	chr7:5638083-5638092 chr7:5638091-5638100
38	CTCF	chr7:5638420-5638570	AG04449	skin:	n/a	chr7:5638522-5638535
39	JUND	chr7:5638397-5638882	K562	blood:	n/a	n/a
40	CHD2	chr7:5637984-5638993	K562	blood:	n/a	n/a
41	TBL1XR1	chr7:5638224-5638841	K562	blood:	n/a	n/a
42	BCL3	chr7:5638204-5638927	K562	blood:	n/a	n/a
43	NR2F2	chr7:5638353-5638801	K562	blood:	n/a	n/a
44	POLR2A	chr7:5637367-5640337	GM12878	blood:	n/a	n/a
45	HMGN3	chr7:5638322-5638977	K562	blood:	n/a	n/a
46	HCFC1	chr7:5638084-5638846	K562	blood:	n/a	n/a
47	TBL1XR1	chr7:5638423-5639010	K562	blood:	n/a	n/a
48	NR2F2	chr7:5637691-5639153	K562	blood:	n/a	n/a
49	POLR2A	chr7:5637413-5638701	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr7:5637398-5638722	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:26213863..26216212-chr7:5636879..5638961,2	K562	blood:
2	chr7:5596314..5597931-chr7:5637976..5640574,2	MCF-7	breast:
3	chr7:5561309..5562941-chr7:5638021..5639699,2	K562	blood:
4	chr7:5531779..5533784-chr7:5636473..5638902,3	K562	blood:
5	chr7:5598398..5599043-chr7:5638111..5638794,2	K562	blood:
6	chr7:5601967..5603891-chr7:5638384..5639932,2	MCF-7	breast:
7	chr7:5638174..5640538-chr7:5702436..5704254,2	K562	blood:
8	chr7:5637430..5639674-chr7:5702754..5705008,2	K562	blood:
9	chr7:5563317..5574038-chr7:5630450..5643029,58	K562	blood:
10	chr7:5464118..5465697-chr7:5637454..5640085,2	K562	blood:
11	chr7:5637583..5639274-chr7:5662917..5664580,2	MCF-7	breast:

Variant related genes	Relation type
FSCN1	TF binding region
ENSG00000272953	Chromatin interaction
ENSG00000182095	Chromatin interaction
ENSG00000263900	Chromatin interaction
ENSG00000272719	Chromatin interaction
ENSG00000075624	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10951961	0.83[AMR][1000 genomes]
rs11763027	0.83[AMR][1000 genomes]
rs1628786	1.00[AMR][1000 genomes]
rs1725186	1.00[AMR][1000 genomes]
rs1990835	0.83[AMR][1000 genomes]
rs2161012	0.83[AMR][1000 genomes]
rs2693951	1.00[AMR][1000 genomes]
rs2881234	0.83[AMR][1000 genomes]
rs3943984	0.83[AMR][1000 genomes]
rs4720636	0.83[AMR][1000 genomes]
rs4720639	0.83[AMR][1000 genomes]
rs4724714	0.83[AMR][1000 genomes]
rs4724720	0.83[AMR][1000 genomes]
rs4724721	0.83[AMR][1000 genomes]
rs6463508	0.83[AMR][1000 genomes]
rs6944453	0.83[AMR][1000 genomes]
rs710939	1.00[AMR][1000 genomes]
rs710940	1.00[AMR][1000 genomes]
rs710942	1.00[AMR][1000 genomes]
rs7790499	0.83[AMR][1000 genomes]
rs852260	0.83[AMR][1000 genomes]
rs852262	1.00[AMR][1000 genomes]
rs852264	1.00[AMR][1000 genomes]
rs852377	0.83[AMR][1000 genomes]
rs852381	1.00[AMR][1000 genomes]
rs852383	1.00[AMR][1000 genomes]
rs852398	1.00[AMR][1000 genomes]
rs852399	1.00[AMR][1000 genomes]
rs852401	1.00[AMR][1000 genomes]
rs852404	1.00[AMR][1000 genomes]
rs852407	1.00[AMR][1000 genomes]
rs852408	1.00[AMR][1000 genomes]
rs852412	1.00[AMR][1000 genomes]
rs852413	1.00[AMR][1000 genomes]
rs852416	1.00[AMR][1000 genomes]
rs852419	1.00[AMR][1000 genomes]
rs852437	0.85[AMR][1000 genomes]
rs852440	0.85[AMR][1000 genomes]
rs852443	1.00[AMR][1000 genomes]
rs852449	1.00[AMR][1000 genomes]
rs852451	1.00[AMR][1000 genomes]
rs852458	1.00[AMR][1000 genomes]
rs852462	0.85[AMR][1000 genomes]
rs852465	1.00[AMR][1000 genomes]
rs852475	0.85[AMR][1000 genomes]
rs852476	1.00[AMR][1000 genomes]
rs852485	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs852486	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs852487	0.85[AMR][1000 genomes]
rs852490	1.00[AMR][1000 genomes]
rs852495	1.00[AMR][1000 genomes]
rs852509	0.85[AMR][1000 genomes]
rs852518	1.00[AMR][1000 genomes]
rs852523	1.00[AMR][1000 genomes]
rs852524	1.00[AMR][1000 genomes]
rs852525	1.00[AMR][1000 genomes]
rs852536	1.00[AMR][1000 genomes]
rs852541	1.00[AMR][1000 genomes]
rs852543	1.00[AMR][1000 genomes]
rs852544	1.00[AMR][1000 genomes]
rs941016	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
2	nsv530979	chr7:5101631-5864814	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
3	nsv530981	chr7:5157150-5920006	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
4	esv1814049	chr7:5314993-5675131	Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	333 gene(s)	inside rSNPs	diseases
5	esv1820266	chr7:5332088-5665173	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
6	nsv530983	chr7:5370746-6070852	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
7	nsv887404	chr7:5402606-5667645	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	331 gene(s)	inside rSNPs	diseases
8	nsv916391	chr7:5417945-5889565	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	336 gene(s)	inside rSNPs	diseases
9	nsv887408	chr7:5432672-5667645	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	331 gene(s)	inside rSNPs	diseases
10	nsv830890	chr7:5464933-5705158	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
11	nsv533108	chr7:5488018-6316581	Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	390 gene(s)	inside rSNPs	diseases
12	nsv1025434	chr7:5537571-5705283	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	297 gene(s)	inside rSNPs	diseases
13	nsv482449	chr7:5557585-5743673	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
14	nsv1033556	chr7:5565080-6186815	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
15	nsv538710	chr7:5565080-6186815	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
16	nsv887414	chr7:5584934-5667645	Flanking Bivalent TSS/Enh Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
17	nsv887415	chr7:5584934-5675305	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
18	nsv887416	chr7:5584934-5695259	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
19	nsv530467	chr7:5617816-5815082	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
20	nsv1017612	chr7:5629728-5819144	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
21	nsv1021989	chr7:5629728-6186815	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:5634400-5639600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr7:5634800-5640200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr7:5635600-5639400	Enhancers	Spleen	Spleen
4	chr7:5635800-5642800	Weak transcription	Aorta	Aorta
5	chr7:5636000-5639800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr7:5636200-5639200	Enhancers	Fetal Brain Male	brain
7	chr7:5636200-5639600	Enhancers	H1 Cell Line	embryonic stem cell
8	chr7:5636200-5642600	Weak transcription	HepG2	liver
9	chr7:5636200-5662000	Weak transcription	Fetal Kidney	kidney
10	chr7:5636400-5638600	Enhancers	Stomach Smooth Muscle	stomach
11	chr7:5636400-5638800	Enhancers	Fetal Lung	lung
12	chr7:5636400-5639000	Enhancers	Adipose Nuclei	Adipose
13	chr7:5636400-5639000	Genic enhancers	Fetal Muscle Leg	muscle
14	chr7:5636400-5639600	Genic enhancers	Fetal Stomach	stomach
15	chr7:5636400-5639600	Enhancers	Ovary	ovary
16	chr7:5636400-5639800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr7:5636400-5640200	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr7:5636400-5642600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr7:5636600-5639200	Enhancers	Colonic Mucosa	Colon
20	chr7:5636600-5639200	Genic enhancers	Osteobl	bone
21	chr7:5636600-5639600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr7:5636600-5640000	Genic enhancers	Fetal Muscle Trunk	muscle
23	chr7:5636600-5643400	Weak transcription	Pancreas	Pancrea
24	chr7:5636600-5661400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr7:5636800-5639000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr7:5636800-5639200	Genic enhancers	NHLF	lung
27	chr7:5636800-5639400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr7:5636800-5639800	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr7:5636800-5639800	Enhancers	Brain Substantia Nigra	brain
30	chr7:5636800-5640000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr7:5636800-5643200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr7:5636800-5661200	Weak transcription	Colon Smooth Muscle	Colon
33	chr7:5637200-5638600	Flanking Active TSS	K562	blood
34	chr7:5637200-5639200	Enhancers	Placenta Amnion	Placenta Amnion
35	chr7:5637400-5638800	Enhancers	Right Ventricle	heart
36	chr7:5637400-5639000	Flanking Active TSS	Hela-S3	cervix
37	chr7:5637400-5639000	Flanking Active TSS	HSMM	muscle
38	chr7:5637400-5639200	Enhancers	HSMMtube	muscle
39	chr7:5637400-5639600	Transcr. at gene 5' and 3'	NHEK	skin
40	chr7:5637400-5639800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr7:5637600-5638600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr7:5637600-5638600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
43	chr7:5637600-5638600	Bivalent Enhancer	Fetal Intestine Large	intestine
44	chr7:5637600-5638800	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
45	chr7:5637600-5639000	Enhancers	Primary hematopoietic stem cells	blood
46	chr7:5637600-5639000	Enhancers	Esophagus	oesophagus
47	chr7:5637600-5639000	Enhancers	Lung	lung
48	chr7:5637600-5639000	Enhancers	Rectal Mucosa Donor 29	rectum
49	chr7:5637600-5639000	Flanking Active TSS	A549	lung
50	chr7:5637600-5639000	Flanking Active TSS	GM12878-XiMat	blood

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