Variant report

Variant	rs6843509
Chromosome Location	chr4:120220196-120220197
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:120218971..120221940-chr4:120223972..120225739,2	MCF-7	breast:
2	chr4:120132319..120136069-chr4:120219720..120222326,6	MCF-7	breast:
3	chr4:120133055..120136111-chr4:120217896..120220637,3	MCF-7	breast:
4	chr4:120130951..120136158-chr4:120218006..120223072,8	K562	blood:
5	chr4:120219760..120221715-chr4:120374891..120376939,2	MCF-7	breast:
6	chr4:120210891..120213027-chr4:120219123..120221721,2	K562	blood:
7	chr4:119899594..119901256-chr4:120219092..120221109,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164096	Chromatin interaction
ENSG00000245958	Chromatin interaction
ENSG00000178636	Chromatin interaction
ENSG00000145390	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10006525	0.91[CHD][hapmap]
rs10006706	0.91[CHD][hapmap]
rs10010696	0.80[ASN][1000 genomes]
rs10017335	0.91[CHD][hapmap]
rs10029750	0.82[ASN][1000 genomes]
rs10031033	0.82[CHB][hapmap]
rs10032299	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1011054	0.86[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs10213342	0.81[ASN][1000 genomes]
rs10518300	0.93[CHD][hapmap]
rs10518328	0.91[CHD][hapmap]
rs1052633	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11098496	0.81[ASN][1000 genomes]
rs11098497	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11098498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11098499	0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs11724758	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11726229	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs11729521	0.91[CHD][hapmap]
rs11729897	0.81[ASN][1000 genomes]
rs11731571	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11732621	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11732686	0.82[CHB][hapmap]
rs11734241	0.91[CHD][hapmap]
rs11734519	0.80[ASN][1000 genomes]
rs11737400	0.82[EUR][1000 genomes]
rs11944880	0.82[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap]
rs12186259	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs12501610	0.81[ASN][1000 genomes]
rs12506395	0.82[ASN][1000 genomes]
rs12508504	0.91[CHD][hapmap]
rs12512517	0.81[ASN][1000 genomes]
rs12711071	0.93[CHD][hapmap]
rs13113112	0.82[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs13113885	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13114751	0.80[ASN][1000 genomes]
rs13116504	0.83[ASN][1000 genomes]
rs13129661	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs13133044	0.83[ASN][1000 genomes]
rs13149954	0.82[EUR][1000 genomes]
rs13435802	0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1480931	0.91[CHD][hapmap]
rs1511015	0.81[ASN][1000 genomes]
rs1511018	0.86[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap]
rs1511019	0.86[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs1511025	0.93[CHD][hapmap]
rs1546505	0.95[CHD][hapmap]
rs1980025	0.93[CHD][hapmap]
rs2036858	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2175383	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2389803	0.91[CHD][hapmap]
rs28374891	0.82[ASN][1000 genomes]
rs28419773	0.83[ASN][1000 genomes]
rs28555550	0.83[ASN][1000 genomes]
rs28580295	0.81[EUR][1000 genomes]
rs2892848	0.91[CHD][hapmap]
rs34585914	0.80[ASN][1000 genomes]
rs34616304	0.81[ASN][1000 genomes]
rs34630083	0.80[ASN][1000 genomes]
rs35197422	0.81[ASN][1000 genomes]
rs35271032	0.80[ASN][1000 genomes]
rs35434465	0.81[ASN][1000 genomes]
rs35643470	0.82[ASN][1000 genomes]
rs35916640	0.80[ASN][1000 genomes]
rs3749591	0.86[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs4145951	0.80[ASN][1000 genomes]
rs62320740	0.82[EUR][1000 genomes]
rs6814412	0.81[ASN][1000 genomes]
rs6822808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6834796	0.89[CHD][hapmap]
rs6837898	0.86[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs6848389	0.91[CHD][hapmap]
rs6849561	0.88[CHD][hapmap]
rs6849889	0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs6857105	0.81[ASN][1000 genomes]
rs7659194	0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs7659403	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7672594	0.93[CHD][hapmap]
rs7685268	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs878372	0.93[CHD][hapmap]
rs9991959	0.93[CHD][hapmap]
rs9999724	0.93[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv428769	chr4:120205572-120363323	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6843509	TRPC3	cis	parietal	SCAN
rs6843509	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL
rs6843509	BBS7	cis	cerebellum	SCAN
rs6843509	BBS7	cis	parietal	SCAN
rs6843509	C4orf3	cis	Whole Blood	GTEx
rs6843509	USP53	cis	parietal	SCAN
rs6843509	RP11-384K6.6	cis	Whole Blood	GTEx
rs6843509	LOC284701///FLJ14186///LOC441124///LOC641693///LOC642788///LOC653056	cis	uninvolved skin	skin_eQTL
rs6843509	LOC645513	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120177000-120220200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:120177000-120220200	Weak transcription	Pancreas	Pancrea
3	chr4:120201200-120220200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:120201200-120220200	Weak transcription	Gastric	stomach
5	chr4:120201400-120220200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:120202000-120220200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:120206600-120220200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr4:120206800-120220200	Weak transcription	Stomach Mucosa	stomach
9	chr4:120214400-120220200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr4:120214400-120220200	Weak transcription	Esophagus	oesophagus
11	chr4:120214400-120220200	Weak transcription	Lung	lung
12	chr4:120217000-120220200	Weak transcription	Spleen	Spleen
13	chr4:120218200-120220200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr4:120218400-120220200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr4:120218400-120220400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:120218400-120220600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr4:120218600-120220200	Weak transcription	Fetal Brain Female	brain
18	chr4:120219000-120220200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr4:120219200-120220200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr4:120219200-120220400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr4:120219200-120220400	Enhancers	Fetal Brain Male	brain
22	chr4:120219200-120220600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr4:120219200-120221600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr4:120219200-120222200	Active TSS	Aorta	Aorta
25	chr4:120219200-120222200	Active TSS	Right Ventricle	heart
26	chr4:120219200-120222400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:120219400-120220200	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr4:120219400-120220200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr4:120219400-120220200	Weak transcription	Placenta	Placenta
30	chr4:120219400-120220200	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr4:120219400-120220200	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr4:120219400-120220200	Weak transcription	Small Intestine	intestine
33	chr4:120219400-120220200	Active TSS	HepG2	liver
34	chr4:120219400-120222000	Active TSS	HMEC	breast
35	chr4:120219400-120222000	Active TSS	HSMMtube	muscle
36	chr4:120219400-120222200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr4:120219400-120222200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr4:120219400-120222400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr4:120219400-120222400	Active TSS	Fetal Intestine Large	intestine
40	chr4:120219400-120222400	Active TSS	NHLF	lung
41	chr4:120219600-120220200	Active TSS	Fetal Intestine Small	intestine
42	chr4:120219600-120220200	Active TSS	Right Atrium	heart
43	chr4:120219600-120220400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr4:120219600-120220400	Flanking Active TSS	NHEK	skin
45	chr4:120219600-120220600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr4:120219600-120220600	Flanking Active TSS	Colon Smooth Muscle	Colon
47	chr4:120219600-120220600	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr4:120219600-120220800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr4:120219600-120222400	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr4:120219800-120220200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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