Variant report

Variant	rs9869648
Chromosome Location	chr3:105596568-105596569
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:105586396..105588232-chr3:105595370..105598050,2	MCF-7	breast:
2	chr3:105595423..105598244-chr3:105600923..105603422,2	K562	blood:
3	chr3:105594821..105597024-chr3:105599746..105602672,2	K562	blood:

Variant related genes	Relation type
ENSG00000114423	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1021858	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1021859	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1039544	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10511246	0.93[CEU][hapmap];0.82[CHB][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11921710	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11924742	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12633854	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1503921	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1867192	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1867195	0.81[CEU][hapmap]
rs1910499	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2089091	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2197209	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3996189	0.88[CEU][hapmap]
rs4447799	0.86[CEU][hapmap]
rs4894840	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4894957	0.88[CEU][hapmap]
rs57520912	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58340800	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6437620	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6437621	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6437624	0.87[CEU][hapmap]
rs6437626	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6767627	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6788366	0.88[CEU][hapmap]
rs6804152	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6807382	0.88[CEU][hapmap]
rs7619449	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7629357	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7634844	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7641825	0.93[CEU][hapmap]
rs7648842	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7649466	0.93[CEU][hapmap];0.86[AMR][1000 genomes]
rs7651784	0.87[CEU][hapmap]
rs9631436	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9657904	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9826886	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9841500	0.87[CEU][hapmap]
rs9846534	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9874600	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.86[EUR][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	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1008564	chr3:105554580-105643435	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1008876	chr3:105554580-105645373	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv877312	chr3:105560638-105916506	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105589000-105601200	Weak transcription	Aorta	Aorta
2	chr3:105589000-105601200	Weak transcription	Thymus	Thymus
3	chr3:105589000-105601200	Weak transcription	NH-A	brain
4	chr3:105589200-105601200	Weak transcription	Colon Smooth Muscle	Colon
5	chr3:105589400-105596800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:105590800-105597000	Weak transcription	Fetal Lung	lung
7	chr3:105595200-105597200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr3:105595200-105597200	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr3:105595400-105596600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:105595400-105597400	Enhancers	Muscle Satellite Cultured Cells	--
11	chr3:105595400-105597600	Enhancers	Primary T cells from cord blood	blood
12	chr3:105595600-105596600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr3:105595600-105596600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:105595600-105596800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:105595600-105597400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:105595600-105597400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:105595600-105597400	Enhancers	Osteobl	bone
18	chr3:105595800-105596600	Enhancers	Primary B cells from peripheral blood	blood
19	chr3:105595800-105596600	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr3:105595800-105597000	Weak transcription	Small Intestine	intestine
21	chr3:105595800-105597600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:105595800-105599400	Weak transcription	Stomach Mucosa	stomach
23	chr3:105596000-105596600	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr3:105596000-105596600	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr3:105596000-105597200	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr3:105596200-105596600	Enhancers	Primary B cells from cord blood	blood
27	chr3:105596200-105596600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:105596200-105596600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:105596200-105596800	Enhancers	GM12878-XiMat	blood
30	chr3:105596200-105597000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:105596200-105597000	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr3:105596200-105597200	Enhancers	Pancreatic Islets	Pancreatic Islet
33	chr3:105596200-105597400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr3:105596200-105597600	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr3:105596200-105597600	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr3:105596200-105601200	Weak transcription	Fetal Kidney	kidney
37	chr3:105596400-105596600	Enhancers	Primary hematopoietic stem cells	blood
38	chr3:105596400-105596600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr3:105596400-105596600	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr3:105596400-105597200	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr3:105596400-105597400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:105596400-105597600	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr3:105596400-105601200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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