Variant report

Variant	rs1883325
Chromosome Location	chr6:11806076-11806077
allele	G/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	TBL1XR1	chr6:11805913-11806085	K562	blood:	n/a	n/a
2	FOS	chr6:11805596-11806095	MCF10A-Er-Src	breast:	n/a	n/a
3	JUND	chr6:11806028-11806132	K562	blood:	n/a	n/a
4	TAL1	chr6:11805986-11806309	K562	blood:	n/a	n/a
5	EGR1	chr6:11805880-11806227	K562	blood:	n/a	chr6:11806053-11806064 chr6:11806055-11806064 chr6:11806052-11806066 chr6:11806053-11806064
6	MYC	chr6:11805564-11806407	MCF10A-Er-Src	breast:	n/a	chr6:11805654-11805664
7	POLR2A	chr6:11805739-11807125	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr6:11805566-11806186	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr6:11805573-11806138	MCF10A-Er-Src	breast:	n/a	n/a
10	HMGN3	chr6:11805922-11806110	K562	blood:	n/a	n/a
11	POLR2A	chr6:11805016-11807694	MCF10A-Er-Src	breast:	n/a	n/a
12	STAT3	chr6:11805594-11806151	MCF10A-Er-Src	breast:	n/a	chr6:11805706-11805718 chr6:11805782-11805793
13	MYC	chr6:11805484-11806338	MCF10A-Er-Src	breast:	n/a	chr6:11805654-11805664
14	RCOR1	chr6:11805519-11806323	K562	blood:	n/a	n/a
15	RCOR1	chr6:11805856-11806252	K562	blood:	n/a	n/a
16	POLR2A	chr6:11806031-11806111	MCF-7	breast:	n/a	n/a
17	STAT3	chr6:11805626-11806233	MCF10A-Er-Src	breast:	n/a	chr6:11805706-11805718 chr6:11805782-11805793
18	EGR1	chr6:11805887-11806217	K562	blood:	n/a	chr6:11806053-11806064 chr6:11806055-11806064 chr6:11806052-11806066 chr6:11806053-11806064

No.	Distal block	Cell Line	Cell type
1	chr6:11804413..11807277-chr6:11809365..11811580,3	K562	blood:
2	chr6:11804065..11806313-chr6:11822779..11824702,2	MCF-7	breast:
3	chr6:11804488..11807450-chr6:12008603..12011488,3	MCF-7	breast:
4	chr6:11786886..11789714-chr6:11803820..11806163,2	K562	blood:
5	chr6:11801584..11803967-chr6:11804359..11806565,2	K562	blood:
6	chr6:11803840..11806433-chr6:11820029..11821651,2	K562	blood:

Variant related genes	Relation type
ENSG00000234427	TF binding region
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[AFR][1000 genomes];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]
rs1883326	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2143715	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[EUR][1000 genomes]
rs2179742	0.90[CEU][hapmap]
rs35325311	0.84[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	1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6942235	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];1.00[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:46 , 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	chr6:11802200-11806400	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr6:11802600-11806400	Enhancers	Fetal Intestine Small	intestine
5	chr6:11802800-11809200	Weak transcription	Hela-S3	cervix
6	chr6:11803400-11806600	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr6:11803600-11806800	Weak transcription	Lung	lung
8	chr6:11803800-11807000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:11803800-11809600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr6:11804000-11807200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:11804400-11806200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:11804400-11806400	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr6:11804400-11806600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:11804400-11806600	Enhancers	Colonic Mucosa	Colon
15	chr6:11804400-11807000	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr6:11804600-11807000	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr6:11804800-11806200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:11804800-11806600	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr6:11804800-11806800	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr6:11804800-11807000	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr6:11805000-11806200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:11805000-11807200	Enhancers	H1 Cell Line	embryonic stem cell
23	chr6:11805000-11807200	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr6:11805000-11809800	Weak transcription	Fetal Lung	lung
25	chr6:11805000-11809800	Weak transcription	Osteobl	bone
26	chr6:11805000-11810400	Weak transcription	Right Atrium	heart
27	chr6:11805200-11806400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:11805200-11807600	Enhancers	Dnd41	blood
29	chr6:11805200-11810200	Weak transcription	NH-A	brain
30	chr6:11805400-11806800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:11805400-11807400	Flanking Active TSS	NHEK	skin
32	chr6:11805400-11807600	Enhancers	Esophagus	oesophagus
33	chr6:11805400-11807600	Flanking Active TSS	HMEC	breast
34	chr6:11805400-11809800	Weak transcription	HSMMtube	muscle
35	chr6:11805400-11810200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:11805600-11806400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:11805600-11806600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr6:11805600-11807000	Enhancers	Fetal Intestine Large	intestine
39	chr6:11805600-11808000	Enhancers	Fetal Thymus	thymus
40	chr6:11805800-11806200	Weak transcription	Duodenum Mucosa	Duodenum
41	chr6:11805800-11806400	Flanking Active TSS	K562	blood
42	chr6:11805800-11809800	Weak transcription	Stomach Mucosa	stomach
43	chr6:11806000-11806200	Enhancers	H9 Cell Line	embryonic stem cell
44	chr6:11806000-11806200	Enhancers	Placenta Amnion	Placenta Amnion
45	chr6:11806000-11806400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr6:11806000-11807200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links