Variant report

Variant	rs17012829
Chromosome Location	chr3:23261334-23261335
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:23255785..23258216-chr3:23259980..23262399,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10510536	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11926494	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11927173	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13094957	0.84[CHB][hapmap]
rs13314285	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1495130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1496653	0.95[CHB][hapmap];0.83[CHD][hapmap]
rs17012800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1908475	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017065	0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs2173058	0.95[CHB][hapmap]
rs4327332	0.90[ASN][1000 genomes]
rs56223303	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57131555	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs58724157	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60782093	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61578857	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6765801	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6769167	0.88[ASN][1000 genomes]
rs6792370	0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs73823472	0.82[ASN][1000 genomes]
rs7612463	0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7613185	0.95[CHB][hapmap]
rs7627380	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9831921	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9866739	0.98[ASN][1000 genomes]
rs9867046	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834636	chr3:23138653-23301443	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1014701	chr3:23257658-23416094	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23245800-23262800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:23246200-23264200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr3:23246400-23273400	Weak transcription	Aorta	Aorta
4	chr3:23246600-23262400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:23248800-23265800	Weak transcription	Primary T cells from cord blood	blood
6	chr3:23249000-23273400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:23251600-23262800	Weak transcription	Adipose Nuclei	Adipose
8	chr3:23257000-23263200	Enhancers	Brain Hippocampus Middle	brain
9	chr3:23259000-23261400	Enhancers	A549	lung
10	chr3:23259000-23261400	Enhancers	NHLF	lung
11	chr3:23259000-23262200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr3:23259000-23262600	Enhancers	Colon Smooth Muscle	Colon
13	chr3:23259400-23261600	Enhancers	HSMM	muscle
14	chr3:23259400-23262400	Enhancers	Liver	Liver
15	chr3:23259600-23262000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr3:23260400-23261400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:23260400-23261600	Enhancers	Stomach Mucosa	stomach
18	chr3:23260400-23262400	Enhancers	Osteobl	bone
19	chr3:23260600-23261400	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr3:23260600-23261400	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr3:23260600-23261400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:23260600-23261400	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr3:23260600-23261400	Enhancers	Brain Anterior Caudate	brain
24	chr3:23260600-23261400	Enhancers	Thymus	Thymus
25	chr3:23260600-23261400	Enhancers	Spleen	Spleen
26	chr3:23260600-23261400	Enhancers	HSMMtube	muscle
27	chr3:23260600-23261600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr3:23260600-23261600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:23260600-23261600	Enhancers	Brain Substantia Nigra	brain
30	chr3:23260600-23261600	Enhancers	Duodenum Mucosa	Duodenum
31	chr3:23260600-23261600	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr3:23260600-23261600	Flanking Active TSS	GM12878-XiMat	blood
33	chr3:23260600-23262400	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr3:23260800-23261400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:23260800-23262200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr3:23260800-23262600	Enhancers	Primary B cells from peripheral blood	blood
37	chr3:23260800-23262600	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr3:23260800-23270400	Weak transcription	Psoas Muscle	Psoas
39	chr3:23260800-23273400	Weak transcription	Right Atrium	heart
40	chr3:23261000-23261400	Enhancers	Brain Angular Gyrus	brain
41	chr3:23261000-23262400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr3:23261000-23262600	Enhancers	Primary B cells from cord blood	blood
43	chr3:23261000-23273400	Weak transcription	Ovary	ovary
44	chr3:23261000-23274400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr3:23261200-23261400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:23261200-23261400	Enhancers	NH-A	brain
47	chr3:23261200-23262400	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr3:23261200-23262600	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr3:23261200-23264800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr3:23261200-23272600	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links