Variant report

Variant	rs12487763
Chromosome Location	chr3:47006884-47006885
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46992891..46995361-chr3:47004607..47007374,2	MCF-7	breast:
2	chr3:47004144..47011042-chr3:47018115..47025018,10	MCF-7	breast:
3	chr3:46970325..46973197-chr3:47005456..47008384,2	MCF-7	breast:
4	chr3:47000539..47004616-chr3:47005854..47010349,8	K562	blood:

Variant related genes	Relation type
ENSG00000160799	Chromatin interaction
ENSG00000160796	Chromatin interaction

Extended variants
information (count: 161 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:151)

rs_ID	r²[population]
rs10461017	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10461019	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10865945	1.00[EUR][1000 genomes]
rs11130108	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11130109	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11706212	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11708257	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11709693	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11709876	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11713537	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11922925	1.00[EUR][1000 genomes]
rs11928558	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12330516	1.00[EUR][1000 genomes]
rs12488371	1.00[EUR][1000 genomes]
rs13062185	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13062516	0.84[AFR][1000 genomes]
rs13078181	1.00[EUR][1000 genomes]
rs13079416	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13082531	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13323092	1.00[EUR][1000 genomes]
rs1378818	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1463394	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1466272	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1466273	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1466274	1.00[AMR][1000 genomes]
rs1473382	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1473384	1.00[EUR][1000 genomes]
rs1473385	1.00[EUR][1000 genomes]
rs1563431	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1563432	1.00[EUR][1000 genomes]
rs1814564	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1869870	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1874264	1.00[EUR][1000 genomes]
rs1979736	1.00[EUR][1000 genomes]
rs2124509	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2124510	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2350642	1.00[EUR][1000 genomes]
rs2385863	1.00[EUR][1000 genomes]
rs2385868	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2385869	0.89[AMR][1000 genomes]
rs2385872	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs28735306	1.00[EUR][1000 genomes]
rs2891887	0.89[AMR][1000 genomes]
rs2891893	0.86[AFR][1000 genomes]
rs34147581	1.00[EUR][1000 genomes]
rs35366910	1.00[EUR][1000 genomes]
rs4018904	1.00[EUR][1000 genomes]
rs4282092	1.00[EUR][1000 genomes]
rs4289375	0.81[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4324490	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4373094	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4378998	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4389512	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4450857	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4478107	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4522803	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4525902	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4543047	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682828	1.00[EUR][1000 genomes]
rs4682832	0.81[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682833	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682834	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4682835	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682836	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682838	0.82[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682841	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682843	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682846	1.00[EUR][1000 genomes]
rs4682847	1.00[EUR][1000 genomes]
rs4683277	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683279	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683283	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683284	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683285	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683286	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683288	1.00[EUR][1000 genomes]
rs4683289	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683290	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683291	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683292	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683293	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683303	1.00[EUR][1000 genomes]
rs6442041	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442042	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442043	0.82[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442044	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442047	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442048	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442062	1.00[EUR][1000 genomes]
rs6442063	1.00[EUR][1000 genomes]
rs6766676	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6767868	1.00[EUR][1000 genomes]
rs6768169	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6775797	1.00[EUR][1000 genomes]
rs6780994	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6785462	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6804732	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6806521	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808052	1.00[EUR][1000 genomes]
rs6808117	1.00[EUR][1000 genomes]
rs6808629	1.00[EUR][1000 genomes]
rs6809904	0.82[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831482	1.00[EUR][1000 genomes]
rs7615774	1.00[EUR][1000 genomes]
rs7621530	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7624549	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7625011	0.83[AFR][1000 genomes]
rs7630154	1.00[EUR][1000 genomes]
rs7630904	0.82[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7631423	0.83[AFR][1000 genomes]
rs7638549	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7641494	1.00[EUR][1000 genomes]
rs7643150	1.00[EUR][1000 genomes]
rs7643868	0.82[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7644382	1.00[EUR][1000 genomes]
rs7646076	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7649413	1.00[EUR][1000 genomes]
rs7649941	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7650142	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7652492	1.00[EUR][1000 genomes]
rs880155	1.00[CHB][hapmap]
rs936173	1.00[EUR][1000 genomes]
rs936177	0.82[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936178	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936179	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936180	0.81[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936181	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936182	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936185	1.00[EUR][1000 genomes]
rs936186	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9637426	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9810881	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9812407	1.00[EUR][1000 genomes]
rs9819344	1.00[EUR][1000 genomes]
rs9819475	1.00[EUR][1000 genomes]
rs9823480	1.00[EUR][1000 genomes]
rs9826488	1.00[EUR][1000 genomes]
rs9827293	1.00[EUR][1000 genomes]
rs9828473	1.00[EUR][1000 genomes]
rs9833500	1.00[EUR][1000 genomes]
rs9836801	1.00[EUR][1000 genomes]
rs9850151	1.00[EUR][1000 genomes]
rs9852167	1.00[EUR][1000 genomes]
rs9861247	1.00[EUR][1000 genomes]
rs9861265	1.00[EUR][1000 genomes]
rs9862711	1.00[EUR][1000 genomes]
rs9869489	1.00[EUR][1000 genomes]
rs9878813	1.00[EUR][1000 genomes]
rs9883152	1.00[EUR][1000 genomes]
rs9883909	1.00[EUR][1000 genomes]
rs9990284	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv3800	chr3:46961648-47007241	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1012682	chr3:46973552-47016357	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	nsv1009396	chr3:46994991-47048166	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46996000-47007200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr3:47002200-47012000	Weak transcription	Osteobl	bone
3	chr3:47002400-47007400	Weak transcription	Colonic Mucosa	Colon
4	chr3:47002400-47012000	Weak transcription	NHLF	lung
5	chr3:47002400-47013200	Weak transcription	NH-A	brain
6	chr3:47003000-47007000	Weak transcription	HSMMtube	muscle
7	chr3:47003000-47007200	Weak transcription	Hela-S3	cervix
8	chr3:47003000-47010400	Weak transcription	Aorta	Aorta
9	chr3:47003200-47011800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:47003200-47012000	Weak transcription	Brain Angular Gyrus	brain
11	chr3:47003200-47012000	Weak transcription	NHDF-Ad	bronchial
12	chr3:47003200-47015800	Weak transcription	Fetal Brain Male	brain
13	chr3:47003200-47016800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:47003400-47008600	Weak transcription	Brain Substantia Nigra	brain
15	chr3:47003400-47012000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:47004200-47007000	Weak transcription	Primary T cells from cord blood	blood
17	chr3:47004400-47011800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:47004600-47007200	Weak transcription	Fetal Heart	heart
19	chr3:47004800-47007000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:47004800-47007200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:47004800-47011800	Weak transcription	HUVEC	blood vessel
22	chr3:47004800-47012000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:47004800-47012600	Weak transcription	HSMM	muscle
24	chr3:47004800-47017200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr3:47004800-47017200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:47005000-47008400	Weak transcription	HMEC	breast
27	chr3:47005600-47008400	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr3:47006400-47007000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:47006400-47007000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr3:47006400-47007200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:47006400-47007400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr3:47006400-47007400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr3:47006400-47009600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:47006400-47010600	Genic enhancers	Primary hematopoietic stem cells	blood
35	chr3:47006400-47011200	Enhancers	Liver	Liver
36	chr3:47006400-47011400	Genic enhancers	HepG2	liver
37	chr3:47006400-47012600	Genic enhancers	Primary B cells from peripheral blood	blood
38	chr3:47006400-47013000	Genic enhancers	K562	blood
39	chr3:47006400-47013200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr3:47006400-47013600	Genic enhancers	Fetal Intestine Small	intestine
41	chr3:47006600-47007000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:47006600-47007000	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr3:47006600-47007000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:47006600-47007000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:47006600-47007000	Genic enhancers	Muscle Satellite Cultured Cells	--
46	chr3:47006600-47007000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:47006600-47007000	Enhancers	Colon Smooth Muscle	Colon
48	chr3:47006600-47007000	Strong transcription	Fetal Stomach	stomach
49	chr3:47006600-47007000	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr3:47006600-47007200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links