Variant report

Variant	rs6475620
Chromosome Location	chr9:22211203-22211204
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:21811542..21813973-chr9:22210354..22213291,2	MCF-7	breast:
2	chr9:22073696..22075332-chr9:22210353..22212628,2	MCF-7	breast:
3	chr9:22100284..22102861-chr9:22210891..22213800,3	MCF-7	breast:
4	chr9:22107143..22109663-chr9:22210637..22212832,3	MCF-7	breast:
5	chr9:22139653..22143239-chr9:22209012..22211720,3	MCF-7	breast:
6	chr9:22036747..22039495-chr9:22210227..22211780,2	MCF-7	breast:
7	chr9:22205089..22207318-chr9:22210681..22212852,2	MCF-7	breast:
8	chr9:22084880..22086467-chr9:22209801..22211580,2	MCF-7	breast:
9	chr9:22102906..22108968-chr9:22209587..22214559,10	MCF-7	breast:
10	chr9:22165022..22167928-chr9:22210617..22213542,2	MCF-7	breast:
11	chr9:22134989..22139400-chr9:22207897..22213962,14	MCF-7	breast:
12	chr9:22155649..22159842-chr9:22208995..22214201,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000229298	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11788928	0.95[EUR][1000 genomes]
rs11790978	0.90[EUR][1000 genomes]
rs11792798	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11792897	1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs11792932	1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12003808	0.90[EUR][1000 genomes]
rs16905769	1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs2025797	0.90[EUR][1000 genomes]
rs2383209	1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs2383212	0.86[EUR][1000 genomes]
rs4461984	0.90[EUR][1000 genomes]
rs4540492	0.85[EUR][1000 genomes]
rs4621906	0.85[EUR][1000 genomes]
rs4644346	0.85[EUR][1000 genomes]
rs62555449	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62555450	0.90[EUR][1000 genomes]
rs62555451	0.90[EUR][1000 genomes]
rs62555452	0.85[EUR][1000 genomes]
rs62555455	0.81[EUR][1000 genomes]
rs62559460	0.85[EUR][1000 genomes]
rs62559467	0.85[EUR][1000 genomes]
rs62559468	0.90[EUR][1000 genomes]
rs62559469	0.85[EUR][1000 genomes]
rs62559470	0.85[EUR][1000 genomes]
rs62559471	0.85[EUR][1000 genomes]
rs62559472	0.86[EUR][1000 genomes]
rs62559473	0.86[EUR][1000 genomes]
rs62559474	0.86[EUR][1000 genomes]
rs62559475	0.86[EUR][1000 genomes]
rs7035115	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs73442947	1.00[EUR][1000 genomes]
rs73444955	0.85[EUR][1000 genomes]
rs736723	1.00[EUR][1000 genomes]
rs7848967	1.00[EUR][1000 genomes]
rs7853566	0.90[EUR][1000 genomes]
rs7859353	1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs7859407	0.86[EUR][1000 genomes]
rs7872728	0.85[EUR][1000 genomes]
rs943399	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv531617	chr9:21985057-22809676	Genic enhancers Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv892749	chr9:22125913-22244280	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1021264	chr9:22159622-22293804	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1033789	chr9:22183150-22266091	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1029289	chr9:22193167-23023688	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1016067	chr9:22210874-22432654	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:22200800-22216600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:22208400-22212800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:22208400-22212800	Enhancers	HMEC	breast
4	chr9:22208600-22213600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr9:22208600-22214600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr9:22208600-22217200	Enhancers	HSMMtube	muscle
7	chr9:22208800-22218000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr9:22209200-22211800	Weak transcription	Small Intestine	intestine
9	chr9:22209200-22213000	Enhancers	HUVEC	blood vessel
10	chr9:22209400-22211400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr9:22209400-22211400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr9:22209400-22211800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr9:22209400-22212200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr9:22209400-22215000	Enhancers	HSMM	muscle
15	chr9:22209400-22215800	Enhancers	Muscle Satellite Cultured Cells	--
16	chr9:22209400-22216400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr9:22209400-22216800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr9:22209400-22217000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr9:22209400-22217600	Enhancers	NHDF-Ad	bronchial
20	chr9:22209400-22218400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:22209600-22211400	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr9:22209600-22211800	Weak transcription	Adipose Nuclei	Adipose
23	chr9:22209600-22213000	Enhancers	NHEK	skin
24	chr9:22209600-22215200	Enhancers	Osteobl	bone
25	chr9:22209600-22216600	Enhancers	Hela-S3	cervix
26	chr9:22209800-22211400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr9:22209800-22214200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr9:22210200-22212800	Enhancers	NH-A	brain
29	chr9:22210200-22213000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr9:22210200-22215200	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr9:22210400-22211400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr9:22210400-22212800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr9:22210400-22213000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr9:22211000-22211400	Enhancers	NHLF	lung
35	chr9:22211000-22212200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:22211000-22212800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr9:22211000-22213000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr9:22211200-22211400	Enhancers	Rectal Smooth Muscle	rectum
39	chr9:22211200-22212000	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr9:22211200-22212200	Weak transcription	HepG2	liver
41	chr9:22211200-22212400	Transcr. at gene 5' and 3'	A549	lung
42	chr9:22211200-22212600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr9:22211200-22213000	Enhancers	Breast Myoepithelial Primary Cells	Breast

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