Variant report

Variant	rs2251604
Chromosome Location	chr9:79007811-79007812
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	chr9:79007540..79010172-chr9:79074126..79075718,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187210	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10121699	0.82[ASN][1000 genomes]
rs10124695	0.82[ASN][1000 genomes]
rs10125012	0.82[AFR][1000 genomes]
rs10125667	0.84[AFR][1000 genomes]
rs10869767	0.98[ASN][1000 genomes]
rs10869773	0.95[ASN][1000 genomes]
rs11144864	0.96[ASN][1000 genomes]
rs11144865	0.96[ASN][1000 genomes]
rs11144866	0.83[ASN][1000 genomes]
rs11144871	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11144880	0.96[ASN][1000 genomes]
rs11788095	0.81[ASN][1000 genomes]
rs12057052	0.84[ASN][1000 genomes]
rs13288968	0.80[ASN][1000 genomes]
rs13295433	0.95[ASN][1000 genomes]
rs13302654	0.94[ASN][1000 genomes]
rs1535845	0.82[ASN][1000 genomes]
rs1961995	0.84[ASN][1000 genomes]
rs2002423	0.87[ASN][1000 genomes]
rs2377639	0.96[ASN][1000 genomes]
rs2377641	0.83[AFR][1000 genomes]
rs2490573	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2490574	0.82[ASN][1000 genomes]
rs2490576	0.84[ASN][1000 genomes]
rs2490579	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490583	0.88[ASN][1000 genomes]
rs2490584	0.88[ASN][1000 genomes]
rs2490586	0.85[ASN][1000 genomes]
rs2501920	0.82[ASN][1000 genomes]
rs2501922	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2501923	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2501925	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2501927	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2501928	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2501930	0.82[ASN][1000 genomes]
rs2501932	0.82[ASN][1000 genomes]
rs2501933	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501935	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35837300	0.84[ASN][1000 genomes]
rs3739729	1.00[ASN][1000 genomes]
rs4372070	0.97[ASN][1000 genomes]
rs4745541	0.99[ASN][1000 genomes]
rs4745544	0.82[ASN][1000 genomes]
rs6560517	0.95[ASN][1000 genomes]
rs7035385	0.84[AFR][1000 genomes]
rs7847608	0.82[ASN][1000 genomes]
rs7849239	0.95[ASN][1000 genomes]
rs7861089	0.95[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:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:78986600-79008400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:78988200-79008400	Weak transcription	Brain Substantia Nigra	brain
3	chr9:78988200-79008400	Weak transcription	Fetal Heart	heart
4	chr9:78988600-79008200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:78988800-79008400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr9:78990200-79008400	Weak transcription	Right Ventricle	heart
7	chr9:78990400-79008200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr9:78990400-79008400	Weak transcription	Fetal Kidney	kidney
9	chr9:78990600-79008400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr9:78990600-79008400	Weak transcription	Fetal Lung	lung
11	chr9:78990600-79008400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr9:78990800-79008400	Weak transcription	NHLF	lung
13	chr9:78992200-79008600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:78995200-79008400	Weak transcription	Stomach Mucosa	stomach
15	chr9:78995200-79008600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr9:78996000-79008400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr9:78997600-79008400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr9:78997800-79008400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr9:78998400-79008400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr9:78998800-79008600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr9:78999200-79008400	Weak transcription	NH-A	brain
22	chr9:78999400-79008600	Weak transcription	Spleen	Spleen
23	chr9:79000200-79008400	Weak transcription	Pancreas	Pancrea
24	chr9:79000400-79008400	Weak transcription	Thymus	Thymus
25	chr9:79002000-79008400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr9:79003000-79008200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr9:79003000-79008400	Weak transcription	Aorta	Aorta
28	chr9:79003000-79008400	Weak transcription	Left Ventricle	heart
29	chr9:79003000-79008600	Weak transcription	Esophagus	oesophagus
30	chr9:79003400-79008400	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr9:79003400-79008400	Weak transcription	Placenta	Placenta
32	chr9:79003600-79008000	Weak transcription	Fetal Muscle Trunk	muscle
33	chr9:79003600-79008200	Weak transcription	HSMMtube	muscle
34	chr9:79003600-79008400	Weak transcription	Brain Germinal Matrix	brain
35	chr9:79003600-79008400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr9:79003800-79008400	Weak transcription	Osteobl	bone
37	chr9:79004000-79008200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr9:79004200-79008000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr9:79004200-79008000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr9:79004200-79008200	Weak transcription	Colon Smooth Muscle	Colon
41	chr9:79004200-79008400	Weak transcription	Primary T cells from cord blood	blood
42	chr9:79004200-79008400	Weak transcription	Fetal Thymus	thymus
43	chr9:79004200-79008400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr9:79004400-79008400	Weak transcription	Primary B cells from cord blood	blood
45	chr9:79004400-79008400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr9:79004400-79008400	Weak transcription	Psoas Muscle	Psoas
47	chr9:79004600-79008400	Weak transcription	Fetal Stomach	stomach
48	chr9:79006000-79008400	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr9:79007000-79008400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr9:79007200-79008000	Flanking Active TSS	HepG2	liver

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