Variant report

Variant	rs6479578
Chromosome Location	chr9:97631805-97631806
allele	A/G
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:97627475..97632236-chr9:97687625..97689828,4	MCF-7	breast:
2	chr9:97630487..97632741-chr9:97640057..97642082,2	MCF-7	breast:
3	chr9:97630097..97631954-chr9:97679073..97680785,2	MCF-7	breast:
4	chr9:97621507..97626749-chr9:97626893..97633201,8	MCF-7	breast:
5	chr9:97545898..97547763-chr9:97631465..97634095,2	MCF-7	breast:
6	chr9:97626345..97628625-chr9:97631540..97633736,2	K562	blood:
7	chr9:97586655..97589155-chr9:97630334..97631988,2	MCF-7	breast:
8	chr9:97631226..97633221-chr9:97637766..97639575,2	MCF-7	breast:
9	chr9:97626766..97634519-chr9:97675095..97684236,17	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10125566	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1020962	1.00[CEU][hapmap]
rs10217441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1038092	1.00[ASW][hapmap];1.00[CEU][hapmap]
rs10732407	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10733756	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10739988	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739990	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10739991	0.85[EUR][1000 genomes]
rs10761360	1.00[ASN][1000 genomes]
rs10761362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs10761363	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10761371	1.00[CEU][hapmap]
rs10821411	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10993386	1.00[EUR][1000 genomes]
rs10993471	1.00[ASW][hapmap]
rs1113967	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12554043	0.88[MEX][hapmap];1.00[TSI][hapmap]
rs12555128	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs1530331	0.88[MEX][hapmap];0.85[TSI][hapmap]
rs1542107	0.88[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1542108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1564235	1.00[CEU][hapmap]
rs1571896	1.00[CEU][hapmap]
rs16911862	0.81[AMR][1000 genomes]
rs1871220	1.00[CEU][hapmap]
rs1888944	1.00[CEU][hapmap]
rs191654	0.85[EUR][1000 genomes]
rs2026399	0.88[MEX][hapmap];1.00[TSI][hapmap]
rs2061798	1.00[CEU][hapmap]
rs2061799	1.00[CEU][hapmap]
rs2061801	1.00[CEU][hapmap]
rs2095069	0.88[MEX][hapmap];1.00[TSI][hapmap]
rs2099868	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2104888	0.81[AMR][1000 genomes]
rs2119953	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2165715	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406897	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2406898	1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2584805	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs2897523	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35322834	0.81[AMR][1000 genomes]
rs356125	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs356128	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs356132	0.85[EUR][1000 genomes]
rs356133	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs356136	0.85[EUR][1000 genomes]
rs356139	0.85[EUR][1000 genomes]
rs356145	0.85[EUR][1000 genomes]
rs356147	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs356148	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs356149	0.85[EUR][1000 genomes]
rs365465	0.85[EUR][1000 genomes]
rs367319	0.85[EUR][1000 genomes]
rs3739748	1.00[CEU][hapmap]
rs3847311	0.85[EUR][1000 genomes]
rs3886568	0.88[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3887267	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs3910730	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4332191	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs438742	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs448899	0.85[EUR][1000 genomes]
rs456276	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs457795	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs4743968	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743970	1.00[ASN][1000 genomes]
rs4743972	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4743973	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4743975	1.00[CEU][hapmap]
rs4743977	1.00[CEU][hapmap]
rs4744382	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744388	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744389	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4744402	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4744421	1.00[CEU][hapmap]
rs555799	0.82[EUR][1000 genomes]
rs562605	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs60120	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs6479569	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs6479574	1.00[CHB][hapmap]
rs6479575	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479577	1.00[ASN][1000 genomes]
rs6479579	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6479581	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6479582	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6479583	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67208365	0.85[EUR][1000 genomes]
rs68090960	0.85[EUR][1000 genomes]
rs7019602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7022963	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7023719	1.00[CEU][hapmap]
rs7025100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs7029570	0.88[MEX][hapmap];0.85[TSI][hapmap]
rs7035166	0.88[MEX][hapmap];0.85[TSI][hapmap]
rs7038891	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7044371	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7047478	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72748596	0.81[AMR][1000 genomes]
rs72750335	0.81[AMR][1000 genomes]
rs7341710	0.85[EUR][1000 genomes]
rs7852844	0.82[EUR][1000 genomes]
rs7855781	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs7864389	0.93[EUR][1000 genomes]
rs7867856	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7869736	1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs894425	1.00[CHB][hapmap]
rs894426	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs894427	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9409805	0.85[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 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	chr9:97624200-97632800	Weak transcription	Thymus	Thymus
2	chr9:97624800-97632800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr9:97625000-97632000	Weak transcription	Primary T cells from cord blood	blood
4	chr9:97625000-97637800	Weak transcription	Primary B cells from cord blood	blood
5	chr9:97625400-97632200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr9:97625600-97632800	Weak transcription	Dnd41	blood
7	chr9:97626000-97638200	Enhancers	HSMM	muscle
8	chr9:97626000-97638400	Enhancers	HSMMtube	muscle
9	chr9:97626200-97632400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr9:97626400-97632800	Weak transcription	Right Ventricle	heart
11	chr9:97626800-97632000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr9:97627200-97638000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr9:97627400-97637800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr9:97628600-97633200	Enhancers	Placenta Amnion	Placenta Amnion
15	chr9:97628600-97641000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr9:97629000-97632400	Enhancers	Stomach Mucosa	stomach
17	chr9:97629200-97634600	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr9:97629200-97635800	Enhancers	HMEC	breast
19	chr9:97629200-97636000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr9:97629600-97632000	Enhancers	Ovary	ovary
21	chr9:97629600-97632200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr9:97629600-97632800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr9:97629600-97635200	Enhancers	Placenta	Placenta
24	chr9:97629800-97632000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr9:97629800-97633200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr9:97630000-97632000	Enhancers	Fetal Lung	lung
27	chr9:97630000-97632000	Enhancers	HepG2	liver
28	chr9:97630000-97632200	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr9:97630000-97632400	Enhancers	NHLF	lung
30	chr9:97630000-97638400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr9:97630000-97645000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr9:97630200-97632200	Enhancers	HUVEC	blood vessel
33	chr9:97630200-97632800	Enhancers	NHEK	skin
34	chr9:97630200-97633600	Enhancers	NH-A	brain
35	chr9:97630200-97634000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr9:97630200-97634400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr9:97630200-97636800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr9:97630200-97637600	Enhancers	Osteobl	bone
39	chr9:97630200-97638000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr9:97630200-97638200	Enhancers	Muscle Satellite Cultured Cells	--
41	chr9:97630200-97638200	Enhancers	NHDF-Ad	bronchial
42	chr9:97630200-97640800	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr9:97630600-97636800	Enhancers	Fetal Heart	heart
44	chr9:97630600-97637800	Weak transcription	Primary hematopoietic stem cells	blood
45	chr9:97630600-97643600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr9:97630800-97632400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr9:97630800-97633200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr9:97630800-97633200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr9:97630800-97635000	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr9:97630800-97637000	Weak transcription	Fetal Intestine Large	intestine

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