Variant report

Variant	rs589561
Chromosome Location	chr9:79120475-79120476
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:79118137..79121617-chr9:79133678..79136692,4	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1057406	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap]
rs11144926	0.84[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]
rs12553343	1.00[CHB][hapmap]
rs2093839	0.92[CHB][hapmap]
rs2282683	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap]
rs557910	0.82[ASN][1000 genomes]
rs707739	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949417	chr9:79078703-79282589	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv893480	chr9:79115844-79222584	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv437089	chr9:79116975-79139590	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79093400-79142800	Weak transcription	Fetal Stomach	stomach
2	chr9:79114400-79122800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr9:79115000-79122600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:79115600-79120800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:79116600-79121200	Weak transcription	Esophagus	oesophagus
6	chr9:79118200-79120600	Strong transcription	HSMM	muscle
7	chr9:79118400-79121000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr9:79118400-79122800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr9:79118600-79120600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr9:79118600-79120600	Weak transcription	Spleen	Spleen
11	chr9:79118600-79122000	Weak transcription	Stomach Mucosa	stomach
12	chr9:79118600-79122600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr9:79118600-79123200	Strong transcription	Osteobl	bone
14	chr9:79118600-79126200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:79118600-79134200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr9:79118800-79120600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr9:79118800-79120600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr9:79118800-79121200	Weak transcription	Colonic Mucosa	Colon
19	chr9:79118800-79121400	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr9:79118800-79121400	Weak transcription	NH-A	brain
21	chr9:79118800-79124600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr9:79118800-79125200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr9:79118800-79125200	Weak transcription	NHDF-Ad	bronchial
24	chr9:79118800-79127600	Weak transcription	HSMMtube	muscle
25	chr9:79118800-79136400	Weak transcription	Gastric	stomach
26	chr9:79118800-79145800	Weak transcription	Primary B cells from peripheral blood	blood
27	chr9:79119000-79120600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr9:79119000-79120600	Weak transcription	Fetal Muscle Leg	muscle
29	chr9:79119000-79120800	Weak transcription	GM12878-XiMat	blood
30	chr9:79119000-79122400	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr9:79119000-79123000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr9:79119000-79123200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr9:79119000-79125200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr9:79119200-79120800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr9:79119200-79121400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr9:79119200-79124800	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr9:79119200-79125200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr9:79119200-79125200	Weak transcription	NHLF	lung
39	chr9:79119200-79127800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr9:79119200-79134000	Weak transcription	Fetal Intestine Small	intestine
41	chr9:79119600-79120600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr9:79119600-79121200	Weak transcription	Primary T cells from cord blood	blood
43	chr9:79119600-79122600	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr9:79119800-79120600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr9:79119800-79121600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr9:79119800-79123800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr9:79119800-79130400	Weak transcription	Primary B cells from cord blood	blood
48	chr9:79119800-79132200	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr9:79120000-79121400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr9:79120000-79127600	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links