Variant report

Variant	rs1716517
Chromosome Location	chr12:65038211-65038212
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:65033725..65035733-chr12:65037658..65039391,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10784417	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784418	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11175483	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11175484	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1147105	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147107	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1244869	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1244873	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1244878	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1245168	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1245169	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1245179	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1245180	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1245181	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1245183	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1245184	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1245185	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1245186	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1245187	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1264485	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1268914	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1270437	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1270836	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1270837	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1272547	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1383117	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1690259	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1690272	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1690273	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1716490	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1716496	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716506	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1795613	0.97[ASN][1000 genomes]
rs1795618	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1795621	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1795622	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1795624	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1795625	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1797677	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1797678	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1797679	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1797684	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1797688	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1797689	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2464347	0.97[ASN][1000 genomes]
rs2620730	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2682714	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2682716	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2682719	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682728	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2701849	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2701850	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7968403	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7971636	0.97[ASN][1000 genomes]
rs7975455	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832443	chr12:64878856-65057265	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv832444	chr12:64981484-65168472	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv559203	chr12:65002969-65199922	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1045216	chr12:65009102-65176894	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv541513	chr12:65009102-65176894	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv469457	chr12:65009243-65195977	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv559204	chr12:65009243-65195977	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:65019800-65047400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:65021400-65043400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr12:65022400-65039600	Weak transcription	Osteobl	bone
4	chr12:65025000-65059600	Weak transcription	Thymus	Thymus
5	chr12:65025200-65044000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr12:65026400-65043200	Weak transcription	Fetal Stomach	stomach
7	chr12:65027400-65041800	Weak transcription	Spleen	Spleen
8	chr12:65027800-65047600	Weak transcription	Psoas Muscle	Psoas
9	chr12:65028200-65047400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:65028400-65038600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr12:65028400-65047400	Weak transcription	NHDF-Ad	bronchial
12	chr12:65028400-65047400	Weak transcription	NHLF	lung
13	chr12:65028600-65056400	Weak transcription	NHEK	skin
14	chr12:65029000-65041800	Weak transcription	Left Ventricle	heart
15	chr12:65029200-65039800	Enhancers	Primary T cells fromperipheralblood	blood
16	chr12:65029200-65041000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr12:65029200-65041600	Weak transcription	Fetal Muscle Leg	muscle
18	chr12:65029600-65042600	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr12:65029600-65044000	Weak transcription	Fetal Lung	lung
20	chr12:65031000-65047600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr12:65031200-65040000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:65031200-65043400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr12:65031200-65043600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr12:65031200-65043800	Weak transcription	Fetal Intestine Small	intestine
25	chr12:65031400-65042600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:65031400-65043400	Weak transcription	Small Intestine	intestine
27	chr12:65032200-65040000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr12:65032200-65040600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr12:65032600-65041800	Weak transcription	Fetal Heart	heart
30	chr12:65033000-65041800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr12:65033000-65052600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr12:65033400-65043200	Weak transcription	HepG2	liver
33	chr12:65033400-65043400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr12:65033600-65059400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr12:65033800-65038600	Weak transcription	K562	blood
36	chr12:65033800-65043800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr12:65034000-65042000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr12:65034000-65043600	Weak transcription	Primary B cells from cord blood	blood
39	chr12:65034200-65043600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr12:65034400-65041000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr12:65034600-65042600	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr12:65034800-65042800	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr12:65035000-65040600	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr12:65035400-65043400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr12:65036000-65041000	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr12:65036400-65041000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr12:65036600-65039200	Enhancers	Primary B cells from peripheral blood	blood
48	chr12:65036800-65038400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:65036800-65038400	Enhancers	Aorta	Aorta
50	chr12:65036800-65039000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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