Variant report

Variant	rs12346482
Chromosome Location	chr9:6955015-6955016
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:6954682..6956612-chr9:6970287..6972358,2	MCF-7	breast:
2	chr9:6952608..6955450-chr9:6959103..6961194,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10117564	0.88[JPT][hapmap]
rs10123354	1.00[EUR][1000 genomes]
rs10124531	1.00[ASN][1000 genomes]
rs10975922	0.90[AMR][1000 genomes]
rs10975931	1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10975932	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12335500	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12335507	1.00[ASN][1000 genomes]
rs12345802	0.97[ASN][1000 genomes]
rs13440172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13440337	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28453377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28632803	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4742272	0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs58288912	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60170601	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7867363	1.00[ASN][1000 genomes]
rs7868655	1.00[ASN][1000 genomes]
rs9657634	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870402	chr9:6565246-7016784	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv1033539	chr9:6566610-7022554	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
3	nsv466111	chr9:6567841-7017391	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
4	nsv613208	chr9:6567841-7017391	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
5	nsv1024831	chr9:6573752-7018641	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
6	nsv892166	chr9:6602821-7222495	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
7	nsv892181	chr9:6680477-7070962	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
8	nsv613252	chr9:6715730-7022554	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv1023906	chr9:6731786-7372132	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv1023461	chr9:6774993-7022554	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv831500	chr9:6847952-6992535	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv831501	chr9:6868099-7058526	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv892184	chr9:6906384-6985602	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv892185	chr9:6929053-7070962	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv1021234	chr9:6933222-7015397	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv870178	chr9:6941584-7060029	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv892186	chr9:6942605-7075305	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv1018732	chr9:6951700-6979382	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6890000-6987200	Weak transcription	Aorta	Aorta
2	chr9:6893800-6981600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr9:6896200-6959000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr9:6912400-6978400	Weak transcription	Esophagus	oesophagus
5	chr9:6921600-6957600	Weak transcription	Thymus	Thymus
6	chr9:6921800-6960400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr9:6922200-6959000	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr9:6922600-6981000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr9:6924600-6957400	Weak transcription	Fetal Thymus	thymus
10	chr9:6931400-6958600	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr9:6931400-6960000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr9:6932800-6985000	Weak transcription	Spleen	Spleen
13	chr9:6936800-6965200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr9:6938800-6960400	Weak transcription	Adipose Nuclei	Adipose
15	chr9:6939400-6955800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr9:6939400-6967200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr9:6939400-6978600	Weak transcription	Lung	lung
18	chr9:6941800-6956800	Weak transcription	Pancreas	Pancrea
19	chr9:6943600-6960000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr9:6944000-6957600	Weak transcription	Primary B cells from cord blood	blood
21	chr9:6945000-6981000	Weak transcription	Liver	Liver
22	chr9:6945200-6960600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr9:6945200-6982600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr9:6946000-6955200	Weak transcription	NHLF	lung
25	chr9:6950000-6960000	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr9:6953000-6982600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr9:6953600-6956000	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr9:6953800-6955200	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr9:6953800-6955200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr9:6953800-6955600	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr9:6953800-6956000	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr9:6953800-6956800	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr9:6953800-6957200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:6953800-6958000	Enhancers	Brain Angular Gyrus	brain
35	chr9:6954000-6955400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr9:6954000-6955400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr9:6954000-6955600	Enhancers	Primary B cells from peripheral blood	blood
38	chr9:6954000-6957000	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr9:6954000-6957600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr9:6954200-6955200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr9:6954200-6956000	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr9:6954200-6956000	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr9:6954200-6960600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:6954200-6968200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr9:6954200-6994800	Weak transcription	Gastric	stomach
46	chr9:6954600-6955600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr9:6954600-6956000	Enhancers	Brain Germinal Matrix	brain
48	chr9:6954600-6956200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr9:6954600-6957200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr9:6954600-6957400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links