Variant report

Variant	rs9388625
Chromosome Location	chr6:128556956-128556957
allele	A/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	FOS	chr6:128556683-128556994	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr6:128556663-128557046	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr6:128556952-128557001	ProgFib	skin:	n/a	n/a
4	E2F4	chr6:128556793-128557002	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr6:128556642-128557004	MCF10A-Er-Src	breast:	n/a	n/a
6	MYC	chr6:128556744-128556979	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr6:128556758-128556958	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr6:128556654-128557066	MCF10A-Er-Src	breast:	n/a	n/a
9	STAT3	chr6:128556742-128556994	MCF10A-Er-Src	breast:	n/a	n/a
10	MYC	chr6:128556669-128556982	MCF10A-Er-Src	breast:	n/a	n/a
11	CEBPB	chr6:128556686-128556963	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:128555804..128558282-chr6:128839206..128841953,2	MCF-7	breast:
2	chr6:128556240..128558926-chr6:128562380..128563926,2	MCF-7	breast:
3	chr6:128475993..128477605-chr6:128555273..128557043,2	K562	blood:

Variant related genes	Relation type
PTPRK	TF binding region
ENSG00000152894	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10485160	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11961542	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12055654	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12055776	0.85[ASN][1000 genomes]
rs1543376	0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs17055441	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17055472	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17055477	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2073161	0.85[ASN][1000 genomes]
rs2076572	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3813371	0.85[ASN][1000 genomes]
rs3813372	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3813373	0.85[ASN][1000 genomes]
rs4140541	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4140542	0.82[ASN][1000 genomes]
rs4243494	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4421217	0.87[ASN][1000 genomes]
rs4483000	0.84[ASN][1000 genomes]
rs4897252	0.84[ASN][1000 genomes]
rs61422755	0.84[ASN][1000 genomes]
rs61583694	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6928143	0.92[ASN][1000 genomes]
rs6933029	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6938118	0.87[ASN][1000 genomes]
rs730202	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73590673	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs742736	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7753945	0.87[ASN][1000 genomes]
rs7755473	0.85[ASN][1000 genomes]
rs7755836	0.96[ASN][1000 genomes]
rs7773849	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9321113	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9372886	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9372887	0.83[ASN][1000 genomes]
rs9375550	0.81[ASN][1000 genomes]
rs9375551	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9375552	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9375554	0.85[ASN][1000 genomes]
rs9375555	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375556	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375557	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375558	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9385452	0.85[ASN][1000 genomes]
rs9385454	0.84[ASN][1000 genomes]
rs9385455	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9388618	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9388619	0.87[ASN][1000 genomes]
rs9388621	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9388622	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9388624	0.85[ASN][1000 genomes]
rs9388626	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9388627	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9398866	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9398867	0.83[ASN][1000 genomes]
rs9398868	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9402023	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9402024	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9402025	0.85[ASN][1000 genomes]
rs9402027	0.85[ASN][1000 genomes]
rs9402028	0.85[ASN][1000 genomes]
rs9402029	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9402030	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9402031	0.84[ASN][1000 genomes]
rs9402032	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9784773	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9784880	0.94[ASN][1000 genomes]

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	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886649	chr6:128399657-128808054	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv886651	chr6:128450019-128565778	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128488200-128565200	Weak transcription	Fetal Stomach	stomach
2	chr6:128492600-128567800	Weak transcription	Ovary	ovary
3	chr6:128506000-128561000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:128520400-128573800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:128522000-128560800	Weak transcription	Primary T cells from cord blood	blood
6	chr6:128527600-128561000	Weak transcription	Esophagus	oesophagus
7	chr6:128528200-128558400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:128528400-128561000	Weak transcription	Fetal Brain Male	brain
9	chr6:128529800-128561000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr6:128531000-128562400	Weak transcription	Aorta	Aorta
11	chr6:128531200-128562400	Weak transcription	HSMMtube	muscle
12	chr6:128531200-128567800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:128531200-128573800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:128532000-128561000	Weak transcription	Osteobl	bone
15	chr6:128536800-128560600	Weak transcription	Fetal Lung	lung
16	chr6:128537200-128561000	Weak transcription	Fetal Muscle Leg	muscle
17	chr6:128537600-128573800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:128539800-128558200	Weak transcription	NH-A	brain
19	chr6:128540200-128559600	Weak transcription	Primary B cells from peripheral blood	blood
20	chr6:128540200-128561000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:128540200-128564800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr6:128540400-128560400	Weak transcription	Fetal Thymus	thymus
23	chr6:128540400-128560400	Weak transcription	HUVEC	blood vessel
24	chr6:128540400-128569400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr6:128540600-128561000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr6:128540800-128562400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:128544200-128562400	Weak transcription	Gastric	stomach
28	chr6:128544200-128563200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr6:128548400-128558400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:128551200-128557400	Strong transcription	Primary B cells from cord blood	blood
31	chr6:128551400-128558400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr6:128551400-128561000	Weak transcription	Right Atrium	heart
33	chr6:128551400-128565800	Weak transcription	Psoas Muscle	Psoas
34	chr6:128551400-128584400	Weak transcription	Pancreas	Pancrea
35	chr6:128551600-128558400	Weak transcription	Brain Anterior Caudate	brain
36	chr6:128552600-128560400	Weak transcription	Fetal Intestine Large	intestine
37	chr6:128552600-128562400	Weak transcription	Fetal Intestine Small	intestine
38	chr6:128553200-128573800	Weak transcription	NHLF	lung
39	chr6:128553400-128564400	Weak transcription	Lung	lung
40	chr6:128553600-128557000	Strong transcription	HSMM	muscle
41	chr6:128553800-128561000	Weak transcription	Duodenum Mucosa	Duodenum
42	chr6:128553800-128570600	Weak transcription	Liver	Liver
43	chr6:128554000-128561000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr6:128554600-128564200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr6:128555000-128561000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:128555000-128564400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr6:128555200-128558400	Weak transcription	Brain Hippocampus Middle	brain
48	chr6:128555200-128558400	Weak transcription	Brain Substantia Nigra	brain
49	chr6:128555200-128561000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:128555200-128561000	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links