Variant report

Variant	rs12683541
Chromosome Location	chr9:6944415-6944416
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	chr9:6931770..6934269-chr9:6942265..6944921,2	MCF-7	breast:

Extended variants
information (count: 128 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10975907	0.91[EUR][1000 genomes]
rs10975933	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs11788152	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11788187	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11788687	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11788849	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11789124	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11789248	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11789250	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11790720	0.92[CHB][hapmap];0.92[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11791950	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs11792082	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11792447	1.00[CEU][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11792899	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11794598	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11794707	1.00[CEU][hapmap];0.80[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11794732	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11794838	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12684006	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12684331	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12684647	0.81[CEU][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12685041	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12686116	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12686353	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1340517	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17511187	1.00[CEU][hapmap];0.80[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17511250	1.00[CEU][hapmap];0.80[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17511776	0.96[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17595667	1.00[CEU][hapmap];0.80[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17595843	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17595877	1.00[CEU][hapmap];0.80[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17595898	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17596052	1.00[CEU][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2792235	0.84[CEU][hapmap]
rs2890732	0.81[CEU][hapmap]
rs35490381	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3818891	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3818892	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3818894	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3818895	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3818898	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3818899	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3818900	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3818901	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4537355	0.88[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55686117	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55790433	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55978538	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56036039	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56069635	0.89[EUR][1000 genomes]
rs56185621	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56279813	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56357252	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57005961	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58143962	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58213169	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58307562	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58361204	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58378352	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58977474	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59337249	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59636651	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59999598	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60173310	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60392055	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61204407	0.86[EUR][1000 genomes]
rs61685780	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62533762	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62533769	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62533773	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62533774	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62533787	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62533788	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62533789	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62533790	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62533791	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62533792	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62533794	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62533818	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62533819	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62533820	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62533821	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62533822	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62533823	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62533824	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62533825	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62533827	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62533828	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62533829	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62533830	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62533831	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62533832	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62533833	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62533834	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62533837	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62533838	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62533839	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62533840	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67642242	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67866005	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs68190370	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7025865	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7026899	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7034789	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs7040935	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7042372	0.86[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs72701484	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72701487	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73410616	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7863137	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs818901	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870402	chr9:6565246-7016784	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv1033539	chr9:6566610-7022554	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
3	nsv466111	chr9:6567841-7017391	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
4	nsv613208	chr9:6567841-7017391	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
5	nsv1024831	chr9:6573752-7018641	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
6	nsv892166	chr9:6602821-7222495	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
7	nsv892181	chr9:6680477-7070962	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
8	nsv613252	chr9:6715730-7022554	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv1023906	chr9:6731786-7372132	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv1023461	chr9:6774993-7022554	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv831500	chr9:6847952-6992535	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv831501	chr9:6868099-7058526	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv892184	chr9:6906384-6985602	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv892185	chr9:6929053-7070962	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv1021234	chr9:6933222-7015397	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv870178	chr9:6941584-7060029	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv892186	chr9:6942605-7075305	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6890000-6987200	Weak transcription	Aorta	Aorta
2	chr9:6893800-6981600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr9:6896200-6959000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr9:6912400-6978400	Weak transcription	Esophagus	oesophagus
5	chr9:6921600-6957600	Weak transcription	Thymus	Thymus
6	chr9:6921800-6960400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr9:6922200-6959000	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr9:6922600-6944800	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr9:6922600-6981000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr9:6924600-6957400	Weak transcription	Fetal Thymus	thymus
11	chr9:6929800-6944800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr9:6931400-6958600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr9:6931400-6960000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr9:6932400-6945400	Weak transcription	Fetal Intestine Large	intestine
15	chr9:6932600-6949600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr9:6932800-6944800	Weak transcription	Gastric	stomach
17	chr9:6932800-6955000	Weak transcription	Right Atrium	heart
18	chr9:6932800-6985000	Weak transcription	Spleen	Spleen
19	chr9:6933600-6944600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr9:6936800-6965200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr9:6938800-6960400	Weak transcription	Adipose Nuclei	Adipose
22	chr9:6939200-6945600	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr9:6939400-6944800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr9:6939400-6949000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr9:6939400-6955800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr9:6939400-6967200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr9:6939400-6978600	Weak transcription	Lung	lung
28	chr9:6939600-6947800	Weak transcription	Fetal Lung	lung
29	chr9:6940200-6945200	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr9:6941800-6956800	Weak transcription	Pancreas	Pancrea
31	chr9:6943000-6945200	Enhancers	HUVEC	blood vessel
32	chr9:6943400-6945200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr9:6943400-6945200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr9:6943400-6946200	Enhancers	Osteobl	bone
35	chr9:6943600-6945000	Enhancers	Brain Hippocampus Middle	brain
36	chr9:6943600-6945000	Enhancers	Hela-S3	cervix
37	chr9:6943600-6945200	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr9:6943600-6945200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr9:6943600-6945800	Enhancers	Muscle Satellite Cultured Cells	--
40	chr9:6943600-6946000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr9:6943600-6946000	Enhancers	NHDF-Ad	bronchial
42	chr9:6943600-6946400	Weak transcription	Fetal Intestine Small	intestine
43	chr9:6943600-6954000	Weak transcription	Primary B cells from peripheral blood	blood
44	chr9:6943600-6960000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr9:6943800-6944600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr9:6943800-6945000	Enhancers	Liver	Liver
47	chr9:6943800-6945000	Weak transcription	Left Ventricle	heart
48	chr9:6943800-6945000	Enhancers	HMEC	breast
49	chr9:6943800-6945000	Enhancers	NHEK	skin
50	chr9:6943800-6945200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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