Variant report

Variant	rs2490586
Chromosome Location	chr9:79017488-79017489
allele	A/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: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	chr9:79008991..79011604-chr9:79014498..79020251,6	K562	blood:
2	chr9:79007886..79011336-chr9:79013243..79018063,7	MCF-7	breast:
3	chr9:79008574..79010619-chr9:79015878..79018108,2	MCF-7	breast:
4	chr9:79014853..79017600-chr9:79074234..79077178,2	MCF-7	breast:
5	chr9:79017018..79018917-chr9:79033431..79035407,2	MCF-7	breast:
6	chr9:79017044..79018975-chr9:79065546..79068177,2	MCF-7	breast:
7	chr9:79015879..79018411-chr9:79025794..79028344,2	MCF-7	breast:
8	chr9:79009095..79011288-chr9:79015114..79018669,3	K562	blood:
9	chr9:79016781..79018743-chr9:79034547..79036492,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000233814	Chromatin interaction
ENSG00000135002	Chromatin interaction
ENSG00000187210	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10114106	0.86[YRI][hapmap]
rs10114264	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10121699	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10124695	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10735646	0.81[EUR][1000 genomes]
rs10869767	0.84[ASN][1000 genomes]
rs10869773	0.82[ASN][1000 genomes]
rs10869780	0.85[EUR][1000 genomes]
rs11144864	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11144865	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11144871	0.85[ASN][1000 genomes]
rs11144880	0.83[ASN][1000 genomes]
rs11788095	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12057052	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13288968	0.91[ASN][1000 genomes]
rs13295433	0.82[ASN][1000 genomes]
rs13302654	0.81[ASN][1000 genomes]
rs1535845	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1961995	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2002423	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2251604	0.85[ASN][1000 genomes]
rs2377639	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2490572	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2490573	0.81[ASN][1000 genomes]
rs2490574	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2490576	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2490579	0.85[ASN][1000 genomes]
rs2490583	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2490584	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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501922	0.84[ASN][1000 genomes]
rs2501923	0.85[ASN][1000 genomes]
rs2501925	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2501927	0.85[ASN][1000 genomes]
rs2501928	0.83[ASN][1000 genomes]
rs2501930	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2501932	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2501933	0.81[ASN][1000 genomes]
rs2501935	0.81[ASN][1000 genomes]
rs2501937	0.90[ASN][1000 genomes]
rs2501938	0.90[ASN][1000 genomes]
rs2501939	0.90[ASN][1000 genomes]
rs2501940	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2501942	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3739729	0.85[ASN][1000 genomes]
rs4372070	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4745541	0.84[ASN][1000 genomes]
rs4745544	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4745545	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4745546	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6560517	0.82[ASN][1000 genomes]
rs6560519	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6560522	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7847608	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7849239	0.82[ASN][1000 genomes]
rs7861089	0.82[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:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79010600-79018000	Weak transcription	HUVEC	blood vessel
2	chr9:79010600-79018400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr9:79010600-79019400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr9:79010800-79018400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr9:79010800-79018400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr9:79010800-79018400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr9:79010800-79018400	Weak transcription	NHDF-Ad	bronchial
8	chr9:79011000-79018400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr9:79011000-79018400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr9:79011000-79018400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr9:79011200-79018000	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr9:79011200-79018400	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr9:79015200-79019000	Enhancers	HepG2	liver
14	chr9:79015200-79019600	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr9:79015400-79018200	Enhancers	A549	lung
16	chr9:79015600-79018400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:79015800-79018400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr9:79016000-79018400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr9:79016000-79018400	Weak transcription	Hela-S3	cervix
20	chr9:79016000-79018400	Weak transcription	HMEC	breast
21	chr9:79016000-79018400	Weak transcription	NHEK	skin
22	chr9:79016000-79018600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr9:79016000-79023000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr9:79016800-79018200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr9:79016800-79018400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr9:79016800-79019600	Enhancers	Liver	Liver
27	chr9:79016800-79020000	Enhancers	Fetal Intestine Small	intestine
28	chr9:79017000-79018400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr9:79017200-79018000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr9:79017200-79018000	Weak transcription	NHLF	lung
31	chr9:79017200-79018400	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr9:79017200-79018400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr9:79017200-79018400	Weak transcription	NH-A	brain
34	chr9:79017400-79017800	Weak transcription	Fetal Intestine Large	intestine
35	chr9:79017400-79018200	Enhancers	GM12878-XiMat	blood

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