Variant report

Variant	rs9402030
Chromosome Location	chr6:128561002-128561003
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:128551695..128554319-chr6:128560402..128562022,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152894	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10485160	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11961542	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11968433	0.83[YRI][hapmap]
rs11970637	0.81[YRI][hapmap]
rs12055654	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12055776	0.85[ASN][1000 genomes]
rs1543376	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs17053270	0.83[YRI][hapmap]
rs17055441	0.85[CHD][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17055472	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17055477	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2073161	0.89[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs2076572	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3813371	0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs3813372	0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3813373	0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs4140541	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4140542	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4243494	0.87[CHD][hapmap];0.84[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4421217	0.87[ASN][1000 genomes]
rs4483000	0.89[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.82[LWK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4628122	1.00[TSI][hapmap]
rs4897252	0.83[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs61422755	0.84[ASN][1000 genomes]
rs61583694	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6928143	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6933029	0.84[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6938118	0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs730202	0.93[ASW][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73590673	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs742736	0.86[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs7753945	0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs7755473	0.89[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs7755836	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[ASN][1000 genomes]
rs7773849	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9321113	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9372886	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9372887	0.89[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs9375550	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs9375551	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9375552	0.88[CHD][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9375554	0.88[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];0.85[ASN][1000 genomes]
rs9375555	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375556	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[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];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9385452	0.89[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];0.85[ASN][1000 genomes]
rs9385454	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9385455	0.91[AFR][1000 genomes];0.95[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	0.84[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9388622	0.84[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9388623	1.00[TSI][hapmap]
rs9388624	0.88[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs9388625	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388626	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9388627	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9398865	1.00[TSI][hapmap]
rs9398866	0.84[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9398867	0.89[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs9398868	0.82[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9402023	0.83[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9402024	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9402025	0.89[CHB][hapmap];0.85[CHD][hapmap];0.85[ASN][1000 genomes]
rs9402027	0.89[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs9402028	0.85[ASN][1000 genomes]
rs9402029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9402031	0.81[CHB][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9402032	0.89[CHB][hapmap];0.94[JPT][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9784773	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9784880	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];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:89 , 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	chr6:128520400-128573800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:128531000-128562400	Weak transcription	Aorta	Aorta
5	chr6:128531200-128562400	Weak transcription	HSMMtube	muscle
6	chr6:128531200-128567800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:128531200-128573800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:128537600-128573800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:128540200-128564800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:128540400-128569400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr6:128540800-128562400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:128544200-128562400	Weak transcription	Gastric	stomach
13	chr6:128544200-128563200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:128551400-128565800	Weak transcription	Psoas Muscle	Psoas
15	chr6:128551400-128584400	Weak transcription	Pancreas	Pancrea
16	chr6:128552600-128562400	Weak transcription	Fetal Intestine Small	intestine
17	chr6:128553200-128573800	Weak transcription	NHLF	lung
18	chr6:128553400-128564400	Weak transcription	Lung	lung
19	chr6:128553800-128570600	Weak transcription	Liver	Liver
20	chr6:128554600-128564200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr6:128555000-128564400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:128555200-128584400	Weak transcription	HMEC	breast
23	chr6:128555600-128595800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:128555800-128564800	Weak transcription	Fetal Brain Female	brain
25	chr6:128556600-128564400	Strong transcription	HepG2	liver
26	chr6:128558400-128561200	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr6:128558400-128561400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:128558400-128561400	Enhancers	Brain Substantia Nigra	brain
29	chr6:128558400-128561600	Enhancers	Brain Angular Gyrus	brain
30	chr6:128558400-128561800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:128558400-128562800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:128558800-128562200	Weak transcription	NH-A	brain
33	chr6:128559000-128562800	Enhancers	Brain Hippocampus Middle	brain
34	chr6:128559600-128561600	Enhancers	Brain Anterior Caudate	brain
35	chr6:128559600-128570600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:128559800-128562400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr6:128559800-128562600	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr6:128559800-128565600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr6:128560000-128561200	Weak transcription	Brain Germinal Matrix	brain
40	chr6:128560000-128562200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr6:128560000-128562400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr6:128560000-128562400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr6:128560000-128562600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:128560400-128561200	Genic enhancers	HSMM	muscle
45	chr6:128560400-128561400	Enhancers	Primary hematopoietic stem cells	blood
46	chr6:128560400-128561400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr6:128560400-128561400	Enhancers	Left Ventricle	heart
48	chr6:128560400-128561600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr6:128560400-128561600	Enhancers	Adipose Nuclei	Adipose
50	chr6:128560400-128561800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links