Variant report

Variant	rs6942235
Chromosome Location	chr6:11807229-11807230
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	MYC	chr6:11806923-11807625	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr6:11806731-11807569	MCF10A-Er-Src	breast:	n/a	chr6:11807362-11807373 chr6:11807098-11807106
3	STAT3	chr6:11807003-11807558	MCF10A-Er-Src	breast:	n/a	chr6:11807362-11807373 chr6:11807098-11807106
4	FOS	chr6:11806998-11807415	MCF10A-Er-Src	breast:	n/a	n/a
5	MYC	chr6:11806818-11807571	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr6:11806916-11807664	MCF10A-Er-Src	breast:	n/a	chr6:11807362-11807373 chr6:11807098-11807106
7	STAT3	chr6:11806815-11807547	MCF10A-Er-Src	breast:	n/a	chr6:11807362-11807373 chr6:11807098-11807106
8	FOS	chr6:11806904-11807513	MCF10A-Er-Src	breast:	n/a	chr6:11807411-11807419
9	POLR2A	chr6:11805016-11807694	MCF10A-Er-Src	breast:	n/a	n/a
10	EGR1	chr6:11807120-11807651	HCT-116	colon:	n/a	chr6:11807415-11807425 chr6:11807412-11807427 chr6:11807413-11807427 chr6:11807413-11807426 chr6:11807356-11807380 chr6:11807413-11807426 chr6:11807413-11807426 chr6:11807414-11807425
11	FOS	chr6:11806992-11807540	MCF10A-Er-Src	breast:	n/a	chr6:11807411-11807419
12	FOS	chr6:11806808-11807547	MCF10A-Er-Src	breast:	n/a	chr6:11807411-11807419

No.	Distal block	Cell Line	Cell type
1	chr6:11767330..11770016-chr6:11806756..11808382,2	MCF-7	breast:
2	chr6:11804413..11807277-chr6:11809365..11811580,3	K562	blood:
3	chr6:11804488..11807450-chr6:12008603..12011488,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234427	TF binding region
ENSG00000111863	Chromatin interaction
ENSG00000095951	Chromatin interaction
ENSG00000234427	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1014972	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs10947579	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1569731	0.93[EUR][1000 genomes]
rs1569732	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1569734	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1569735	0.93[EUR][1000 genomes]
rs16871833	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1883324	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs1883325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883326	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2143715	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[EUR][1000 genomes]
rs2179742	0.89[CEU][hapmap]
rs35325311	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs3950186	0.95[CEU][hapmap]
rs4308554	0.95[CEU][hapmap];0.83[CHB][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4310046	0.93[EUR][1000 genomes]
rs4404760	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[EUR][1000 genomes]
rs4557506	0.93[EUR][1000 genomes]
rs4634440	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66805427	0.93[EUR][1000 genomes]
rs6899747	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6910363	0.93[ASN][1000 genomes]
rs6914007	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6936286	0.86[CEU][hapmap]
rs6941812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7739256	0.95[CEU][hapmap]
rs7743245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9368892	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs9470184	0.90[CEU][hapmap]
rs978565	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758036	chr6:11679753-11822351	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759407	chr6:11679753-11822351	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11796400-11810400	Weak transcription	Placenta	Placenta
2	chr6:11799200-11809800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr6:11802800-11809200	Weak transcription	Hela-S3	cervix
4	chr6:11803800-11809600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr6:11805000-11809800	Weak transcription	Fetal Lung	lung
6	chr6:11805000-11809800	Weak transcription	Osteobl	bone
7	chr6:11805000-11810400	Weak transcription	Right Atrium	heart
8	chr6:11805200-11807600	Enhancers	Dnd41	blood
9	chr6:11805200-11810200	Weak transcription	NH-A	brain
10	chr6:11805400-11807400	Flanking Active TSS	NHEK	skin
11	chr6:11805400-11807600	Enhancers	Esophagus	oesophagus
12	chr6:11805400-11807600	Flanking Active TSS	HMEC	breast
13	chr6:11805400-11809800	Weak transcription	HSMMtube	muscle
14	chr6:11805400-11810200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:11805600-11808000	Enhancers	Fetal Thymus	thymus
16	chr6:11805800-11809800	Weak transcription	Stomach Mucosa	stomach
17	chr6:11806200-11807400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
18	chr6:11806200-11807400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr6:11806200-11807400	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr6:11806200-11808200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:11806200-11808600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr6:11806400-11807400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr6:11806400-11807400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:11806400-11809600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr6:11806400-11809800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr6:11806400-11809800	Weak transcription	Fetal Intestine Small	intestine
27	chr6:11806400-11810600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr6:11806600-11807600	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr6:11806600-11807600	Enhancers	Primary T cells from cord blood	blood
30	chr6:11806600-11807600	Enhancers	GM12878-XiMat	blood
31	chr6:11806600-11809800	Weak transcription	Colonic Mucosa	Colon
32	chr6:11806600-11810200	Weak transcription	K562	blood
33	chr6:11807000-11807400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:11807000-11807400	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr6:11807000-11807400	Enhancers	Fetal Muscle Trunk	muscle
36	chr6:11807000-11807400	Enhancers	Spleen	Spleen
37	chr6:11807000-11809800	Weak transcription	NHDF-Ad	bronchial
38	chr6:11807000-11810200	Weak transcription	Fetal Intestine Large	intestine
39	chr6:11807000-11810200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr6:11807200-11807400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:11807200-11808000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:11807200-11811000	Weak transcription	Lung	lung

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