Variant report

Variant	rs4590963
Chromosome Location	chr12:87834013-87834014
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	chr12:87828977..87831928-chr12:87832715..87835394,2	MCF-7	breast:

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10735256	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10735258	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10735261	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10735262	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10735264	1.00[EUR][1000 genomes]
rs10745442	0.88[EUR][1000 genomes]
rs10745444	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10745446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10745448	1.00[EUR][1000 genomes]
rs10745449	1.00[EUR][1000 genomes]
rs10777032	0.88[EUR][1000 genomes]
rs10777033	0.92[AMR][1000 genomes]
rs10777034	0.88[EUR][1000 genomes]
rs10777040	0.81[EUR][1000 genomes]
rs10777042	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10777043	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10777048	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10858592	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10858598	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10858599	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11104443	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11104470	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1353484	1.00[EUR][1000 genomes]
rs1353486	1.00[EUR][1000 genomes]
rs1353487	1.00[EUR][1000 genomes]
rs1353488	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1390604	1.00[EUR][1000 genomes]
rs1390605	1.00[EUR][1000 genomes]
rs1496320	1.00[EUR][1000 genomes]
rs1496321	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2047306	1.00[EUR][1000 genomes]
rs2406753	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2897518	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4147490	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4254148	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4258454	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4269999	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4300469	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4303307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4310691	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4319586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4326883	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4338623	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4372533	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4402386	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4442619	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4466916	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4561282	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4564410	0.88[EUR][1000 genomes]
rs4573770	0.83[EUR][1000 genomes]
rs4576908	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4597138	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4635161	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4842462	1.00[EUR][1000 genomes]
rs4842570	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4842576	1.00[EUR][1000 genomes]
rs5005936	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6538078	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6538079	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6538082	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6538083	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6538087	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6538088	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6538104	1.00[EUR][1000 genomes]
rs6538105	1.00[EUR][1000 genomes]
rs6538106	1.00[EUR][1000 genomes]
rs7305305	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7310810	0.88[EUR][1000 genomes]
rs7311170	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7959041	1.00[EUR][1000 genomes]
rs7962840	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7967687	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7969510	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7969564	0.87[EUR][1000 genomes]
rs7969855	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7970729	0.88[EUR][1000 genomes]
rs7970832	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7974679	0.92[AMR][1000 genomes];0.88[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	nsv430523	chr12:87757132-87865832	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv430525	chr12:87757132-87905532	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv559701	chr12:87801947-87905878	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv3350469	chr12:87802235-87844904	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:87832800-87834400	Enhancers	Stomach Mucosa	stomach
2	chr12:87833000-87834400	Enhancers	Fetal Intestine Small	intestine
3	chr12:87833000-87834600	Enhancers	HUVEC	blood vessel
4	chr12:87833000-87835000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:87833000-87835200	Enhancers	Hela-S3	cervix
6	chr12:87833200-87834600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:87833200-87835000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:87833200-87835000	Enhancers	Fetal Intestine Large	intestine
9	chr12:87833200-87835200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr12:87833200-87835200	Enhancers	NHEK	skin
11	chr12:87833200-87835400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:87833200-87835600	Enhancers	HMEC	breast
13	chr12:87833200-87835800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:87833400-87834400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr12:87833400-87834800	Enhancers	Muscle Satellite Cultured Cells	--
16	chr12:87833400-87835000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:87833400-87835000	Enhancers	HSMM	muscle
18	chr12:87833400-87835400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:87833600-87834200	Enhancers	A549	lung
20	chr12:87833600-87834400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:87833600-87834400	Enhancers	Duodenum Mucosa	Duodenum
22	chr12:87833600-87834400	Enhancers	NHLF	lung
23	chr12:87833600-87834600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:87833600-87834600	Enhancers	NH-A	brain
25	chr12:87833600-87834600	Enhancers	Osteobl	bone
26	chr12:87833600-87835000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:87833600-87835000	Enhancers	HSMMtube	muscle
28	chr12:87834000-87834400	Enhancers	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links