Variant report

Variant	rs2490573
Chromosome Location	chr9:78989528-78989529
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	chr9:78981679..78983727-chr9:78987229..78989632,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10121699	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs10869767	0.93[ASN][1000 genomes]
rs10869773	0.91[ASN][1000 genomes]
rs11144864	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11144865	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.98[ASN][1000 genomes]
rs11144866	0.82[ASN][1000 genomes]
rs11144871	0.94[ASN][1000 genomes]
rs11144880	0.92[ASN][1000 genomes]
rs12057052	0.85[ASN][1000 genomes]
rs12344941	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs13288968	0.86[ASN][1000 genomes]
rs13295433	0.91[ASN][1000 genomes]
rs13302654	1.00[ASN][1000 genomes]
rs1961995	0.86[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2002423	0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2251604	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2377639	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2490572	0.86[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2490574	0.85[ASN][1000 genomes]
rs2490576	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2490579	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2490583	0.82[ASN][1000 genomes]
rs2490584	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2490586	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2501922	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2501923	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501925	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2501927	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501928	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2501930	0.86[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2501932	0.88[ASN][1000 genomes]
rs2501933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2501935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2501937	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2501938	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2501939	0.85[ASN][1000 genomes]
rs35837300	0.80[ASN][1000 genomes]
rs3739729	0.94[ASN][1000 genomes]
rs4372070	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4745541	0.93[ASN][1000 genomes]
rs4745544	1.00[JPT][hapmap]
rs6560517	0.91[ASN][1000 genomes]
rs6560522	0.95[JPT][hapmap]
rs7847608	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs7849239	0.91[ASN][1000 genomes]
rs785936	0.83[GIH][hapmap]
rs7861089	0.91[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	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	nsv893478	chr9:78933874-79101006	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	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

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:78980400-78990000	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr9:78984400-78989600	Enhancers	Hela-S3	cervix
3	chr9:78984600-78993200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:78984800-78989800	Weak transcription	Left Ventricle	heart
5	chr9:78985000-78989600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr9:78985000-78989600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr9:78985000-78989800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr9:78985600-78989600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr9:78986000-78990400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr9:78986600-79008400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr9:78986800-78990400	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr9:78986800-78990600	Enhancers	Liver	Liver
13	chr9:78986800-78990800	Enhancers	Fetal Intestine Large	intestine
14	chr9:78986800-78990800	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr9:78986800-78991000	Enhancers	Fetal Stomach	stomach
16	chr9:78987000-78990000	Enhancers	Small Intestine	intestine
17	chr9:78987000-78990200	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr9:78987000-78990600	Enhancers	Colon Smooth Muscle	Colon
19	chr9:78987000-78990600	Enhancers	Fetal Intestine Small	intestine
20	chr9:78987000-78990600	Enhancers	HepG2	liver
21	chr9:78987000-78991000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr9:78987200-78990400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr9:78987200-78991200	Enhancers	Stomach Mucosa	stomach
24	chr9:78987400-78989600	Weak transcription	HUVEC	blood vessel
25	chr9:78987400-78990000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr9:78987600-79007800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr9:78988000-78989800	Enhancers	Aorta	Aorta
28	chr9:78988000-78990400	Enhancers	Fetal Muscle Leg	muscle
29	chr9:78988200-78989600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr9:78988200-78989800	Weak transcription	Esophagus	oesophagus
31	chr9:78988200-78989800	Weak transcription	Placenta	Placenta
32	chr9:78988200-78989800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr9:78988200-78990000	Weak transcription	HSMM	muscle
34	chr9:78988200-78993200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr9:78988200-79002600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr9:78988200-79003200	Weak transcription	HSMMtube	muscle
37	chr9:78988200-79008400	Weak transcription	Brain Substantia Nigra	brain
38	chr9:78988200-79008400	Weak transcription	Fetal Heart	heart
39	chr9:78988400-78989600	Weak transcription	NHDF-Ad	bronchial
40	chr9:78988400-78989800	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr9:78988400-78989800	Weak transcription	Right Atrium	heart
42	chr9:78988400-78990000	Weak transcription	Adipose Nuclei	Adipose
43	chr9:78988400-78990200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr9:78988400-78999000	Weak transcription	Fetal Muscle Trunk	muscle
45	chr9:78988400-78999000	Weak transcription	Spleen	Spleen
46	chr9:78988400-78999600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr9:78988400-79002200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr9:78988600-78989600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr9:78988600-78989600	Weak transcription	K562	blood
50	chr9:78988600-78989600	Weak transcription	NHLF	lung

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