Variant report

Variant	rs4476879
Chromosome Location	chr6:82526352-82526353
allele	C/G
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	EP300	chr6:82526092-82526630	MCF-7	breast:	n/a	n/a
2	SMC3	chr6:82526223-82526361	HepG2	liver:	n/a	n/a
3	FOXA1	chr6:82526101-82526532	HepG2	liver:	n/a	n/a
4	ZNF217	chr6:82526068-82526588	MCF-7	breast:	n/a	n/a
5	HDAC2	chr6:82526047-82526615	MCF-7	breast:	n/a	n/a
6	FOSL2	chr6:82526027-82526586	MCF-7	breast:	n/a	n/a
7	EP300	chr6:82526076-82526527	HepG2	liver:	n/a	n/a
8	NR2F2	chr6:82525947-82526689	MCF-7	breast:	n/a	n/a
9	FOXM1	chr6:82525999-82526612	MCF-7	breast:	n/a	n/a
10	TCF7L2	chr6:82526195-82526536	Hela-S3	cervix:	n/a	chr6:82526355-82526369
11	NR2F2	chr6:82525919-82526751	MCF-7	breast:	n/a	n/a
12	MYBL2	chr6:82526074-82526584	HepG2	liver:	n/a	n/a
13	NR2F2	chr6:82525986-82526646	HepG2	liver:	n/a	n/a
14	FOXA1	chr6:82526139-82526571	HepG2	liver:	n/a	n/a
15	MAX	chr6:82526079-82526538	MCF-7	breast:	n/a	n/a
16	EP300	chr6:82525996-82526626	MCF-7	breast:	n/a	n/a
17	FOXA2	chr6:82526152-82526445	A549	lung:	n/a	n/a
18	TFAP2C	chr6:82526112-82526441	Hela-S3	cervix:	n/a	chr6:82526259-82526274 chr6:82526244-82526259
19	GATA3	chr6:82526072-82526627	MCF-7	breast:	n/a	chr6:82526499-82526508
20	NR2F2	chr6:82526000-82526488	HepG2	liver:	n/a	n/a
21	TFAP2A	chr6:82526118-82526450	Hela-S3	cervix:	n/a	chr6:82526259-82526273 chr6:82526259-82526274 chr6:82526259-82526273
22	TCF7L2	chr6:82526103-82526643	HepG2	liver:	n/a	chr6:82526355-82526369
23	NFIC	chr6:82526061-82526545	HepG2	liver:	n/a	n/a
24	HDAC2	chr6:82526012-82526634	MCF-7	breast:	n/a	n/a
25	MXI1	chr6:82526093-82526363	HepG2	liver:	n/a	n/a
26	SIN3AK20	chr6:82525829-82526724	MCF-7	breast:	n/a	n/a
27	GATA3	chr6:82526170-82526500	MCF-7	breast:	n/a	n/a
28	TCF7L2	chr6:82526121-82526639	MCF-7	breast:	n/a	chr6:82526355-82526369
29	GATA3	chr6:82525821-82526894	MCF-7	breast:	n/a	chr6:82526499-82526508
30	ARID3A	chr6:82526105-82526655	HepG2	liver:	n/a	n/a
31	FOXA1	chr6:82526015-82526548	HepG2	liver:	n/a	n/a
32	TEAD4	chr6:82526081-82526620	MCF-7	breast:	n/a	n/a
33	EP300	chr6:82526091-82526442	HepG2	liver:	n/a	n/a
34	GATA3	chr6:82525916-82526773	MCF-7	breast:	n/a	chr6:82526499-82526508
35	FOXA1	chr6:82526076-82526582	HepG2	liver:	n/a	n/a
36	TEAD4	chr6:82526013-82526585	HepG2	liver:	n/a	n/a
37	SIN3AK20	chr6:82525453-82526800	MCF-7	breast:	n/a	n/a
38	FOXA2	chr6:82526160-82526476	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:82475840..82480204-chr6:82524356..82527900,4	MCF-7	breast:
2	chr6:82508795..82509784-chr6:82525837..82526689,2	MCF-7	breast:
3	chr6:82507285..82509817-chr6:82524544..82526925,2	MCF-7	breast:
4	chr6:82458586..82464036-chr6:82521971..82527096,10	MCF-7	breast:
5	chr6:82461003..82464432-chr6:82526169..82529766,5	MCF-7	breast:
6	chr6:82476464..82477240-chr6:82525825..82526638,3	MCF-7	breast:
7	chr6:82495383..82498182-chr6:82525424..82528036,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224995	TF binding region
ENSG00000112773	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1034241	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs11961442	0.88[EUR][1000 genomes]
rs11969940	0.88[EUR][1000 genomes]
rs13197670	0.86[EUR][1000 genomes]
rs13212198	0.87[EUR][1000 genomes]
rs13212500	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13214556	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16893463	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16893491	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16893518	1.00[CEU][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes]
rs16893523	0.85[EUR][1000 genomes]
rs16893524	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16893526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16893572	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16893614	0.86[EUR][1000 genomes]
rs1931644	0.82[EUR][1000 genomes]
rs1931646	0.86[EUR][1000 genomes]
rs194618	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs194620	0.86[EUR][1000 genomes]
rs1999630	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34411814	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34663254	0.86[EUR][1000 genomes]
rs34696161	0.84[EUR][1000 genomes]
rs34723068	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35039823	0.82[EUR][1000 genomes]
rs35392002	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35419006	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35538583	0.86[EUR][1000 genomes]
rs56021267	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6454240	1.00[CEU][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs66652550	0.86[EUR][1000 genomes]
rs67263687	0.80[EUR][1000 genomes]
rs72899496	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9341901	0.82[YRI][hapmap]
rs9344225	0.80[YRI][hapmap]
rs9353031	0.82[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830712	chr6:82491029-82654531	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:82517200-82530600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:82519200-82528800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:82522800-82531400	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr6:82523000-82530000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:82523200-82528000	Weak transcription	Primary B cells from cord blood	blood
6	chr6:82523400-82527800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:82523400-82528000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr6:82523800-82527400	Enhancers	Hela-S3	cervix
9	chr6:82523800-82532600	Enhancers	Stomach Mucosa	stomach
10	chr6:82524000-82528000	Weak transcription	Primary B cells from peripheral blood	blood
11	chr6:82524000-82528200	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr6:82524200-82526400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:82524600-82526400	Enhancers	Placenta	Placenta
14	chr6:82524600-82528800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:82524800-82528600	Weak transcription	Right Atrium	heart
16	chr6:82524800-82528800	Weak transcription	Gastric	stomach
17	chr6:82524800-82529000	Weak transcription	NHLF	lung
18	chr6:82525000-82527200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:82525000-82528400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:82525000-82529000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:82525200-82527400	Enhancers	HepG2	liver
22	chr6:82525200-82528200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:82525200-82529000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr6:82525400-82528000	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr6:82525600-82527800	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr6:82526000-82526600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:82526200-82526600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:82526200-82526600	Enhancers	Liver	Liver
29	chr6:82526200-82526600	Enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links