Variant report

Variant	rs2490584
Chromosome Location	chr9:79010993-79010994
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:79009596..79011512-chr9:79033569..79035078,2	MCF-7	breast:
2	chr9:78993024..78994920-chr9:79009980..79012177,2	MCF-7	breast:
3	chr9:79007886..79011336-chr9:79013243..79018063,7	MCF-7	breast:
4	chr9:79009527..79011124-chr9:79074048..79076040,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234618	Chromatin interaction
ENSG00000187210	Chromatin interaction
ENSG00000233814	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10121699	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10124695	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10869767	0.86[ASN][1000 genomes]
rs10869773	0.83[ASN][1000 genomes]
rs11144864	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11144865	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11144871	0.88[ASN][1000 genomes]
rs11144880	0.84[ASN][1000 genomes]
rs11144945	1.00[YRI][hapmap]
rs11788095	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12057052	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13288968	0.90[ASN][1000 genomes]
rs13295433	0.83[ASN][1000 genomes]
rs13302654	0.82[ASN][1000 genomes]
rs1535845	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1961995	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2002423	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2251604	0.88[ASN][1000 genomes]
rs2377639	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2490572	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2490573	0.82[ASN][1000 genomes]
rs2490574	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2490576	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2490579	0.88[ASN][1000 genomes]
rs2490583	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490586	0.90[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2501920	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2501922	0.86[ASN][1000 genomes]
rs2501923	0.88[ASN][1000 genomes]
rs2501925	0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2501927	0.88[ASN][1000 genomes]
rs2501928	0.84[ASN][1000 genomes]
rs2501930	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2501932	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2501933	0.82[ASN][1000 genomes]
rs2501935	0.82[ASN][1000 genomes]
rs2501937	0.88[ASN][1000 genomes]
rs2501938	0.88[ASN][1000 genomes]
rs2501939	0.89[ASN][1000 genomes]
rs3739729	0.88[ASN][1000 genomes]
rs4372070	0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4745541	0.86[ASN][1000 genomes]
rs4745544	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4745545	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4745546	0.88[ASN][1000 genomes]
rs638410	1.00[YRI][hapmap]
rs6560517	0.83[ASN][1000 genomes]
rs6560519	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6560522	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs7847608	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7849239	0.83[ASN][1000 genomes]
rs7861089	0.83[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:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79008400-79011000	Active TSS	Aorta	Aorta
2	chr9:79009800-79011000	Flanking Active TSS	Duodenum Mucosa	Duodenum
3	chr9:79010200-79011000	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr9:79010200-79011000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
5	chr9:79010200-79011000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr9:79010200-79017000	Weak transcription	NH-A	brain
7	chr9:79010400-79014800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:79010600-79011000	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr9:79010600-79011000	Enhancers	Primary T cells from cord blood	blood
10	chr9:79010600-79011000	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr9:79010600-79011000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr9:79010600-79011000	Enhancers	Liver	Liver
13	chr9:79010600-79011000	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr9:79010600-79011000	Enhancers	Fetal Intestine Large	intestine
15	chr9:79010600-79011000	Enhancers	Hela-S3	cervix
16	chr9:79010600-79011200	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr9:79010600-79011400	Enhancers	Fetal Intestine Small	intestine
18	chr9:79010600-79011800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr9:79010600-79012000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr9:79010600-79015200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr9:79010600-79015200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr9:79010600-79015200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr9:79010600-79015200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr9:79010600-79015200	Weak transcription	Placenta	Placenta
25	chr9:79010600-79015400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr9:79010600-79015400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr9:79010600-79015400	Weak transcription	HMEC	breast
28	chr9:79010600-79016600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr9:79010600-79016600	Weak transcription	NHLF	lung
30	chr9:79010600-79017000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr9:79010600-79017000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr9:79010600-79018000	Weak transcription	HUVEC	blood vessel
33	chr9:79010600-79018400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr9:79010600-79019400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr9:79010800-79011000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr9:79010800-79011000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr9:79010800-79011000	Enhancers	HepG2	liver
38	chr9:79010800-79011200	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr9:79010800-79011200	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr9:79010800-79011200	Enhancers	Dnd41	blood
41	chr9:79010800-79014800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr9:79010800-79015000	Weak transcription	GM12878-XiMat	blood
43	chr9:79010800-79015400	Weak transcription	A549	lung
44	chr9:79010800-79018400	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr9:79010800-79018400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr9:79010800-79018400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr9:79010800-79018400	Weak transcription	NHDF-Ad	bronchial

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