Variant report

Variant	rs12660596
Chromosome Location	chr6:144736428-144736429
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:144735323..144737849-chr6:144741560..144744024,3	MCF-7	breast:

Extended variants
information (count: 111 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs12660406	1.00[EUR][1000 genomes]
rs12660513	1.00[EUR][1000 genomes]
rs12660531	1.00[EUR][1000 genomes]
rs12661781	0.89[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12661969	1.00[EUR][1000 genomes]
rs12662267	1.00[EUR][1000 genomes]
rs12662696	1.00[EUR][1000 genomes]
rs12662724	1.00[EUR][1000 genomes]
rs12662786	1.00[EUR][1000 genomes]
rs12662872	1.00[EUR][1000 genomes]
rs12662904	1.00[EUR][1000 genomes]
rs12663172	1.00[EUR][1000 genomes]
rs12663380	1.00[EUR][1000 genomes]
rs12663605	1.00[EUR][1000 genomes]
rs12663851	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12664200	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12664245	1.00[EUR][1000 genomes]
rs12664298	1.00[EUR][1000 genomes]
rs12664304	1.00[EUR][1000 genomes]
rs12665589	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12665850	1.00[EUR][1000 genomes]
rs17073524	1.00[EUR][1000 genomes]
rs17073528	1.00[EUR][1000 genomes]
rs17073529	1.00[EUR][1000 genomes]
rs17073544	1.00[EUR][1000 genomes]
rs17073571	1.00[EUR][1000 genomes]
rs17073580	1.00[EUR][1000 genomes]
rs17073598	1.00[EUR][1000 genomes]
rs17073602	1.00[EUR][1000 genomes]
rs17073610	1.00[EUR][1000 genomes]
rs17073623	1.00[EUR][1000 genomes]
rs17073629	1.00[EUR][1000 genomes]
rs17073631	1.00[EUR][1000 genomes]
rs17073672	1.00[EUR][1000 genomes]
rs17073678	1.00[EUR][1000 genomes]
rs17840301	1.00[EUR][1000 genomes]
rs1998367	1.00[EUR][1000 genomes]
rs34140249	1.00[EUR][1000 genomes]
rs35325795	1.00[EUR][1000 genomes]
rs36007040	1.00[EUR][1000 genomes]
rs3811097	1.00[EUR][1000 genomes]
rs3811098	0.82[JPT][hapmap];1.00[AFR][1000 genomes]
rs4301321	1.00[EUR][1000 genomes]
rs4896714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4896715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4896717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55684976	1.00[EUR][1000 genomes]
rs56820385	1.00[EUR][1000 genomes]
rs57380483	1.00[EUR][1000 genomes]
rs57485302	1.00[EUR][1000 genomes]
rs57679521	1.00[EUR][1000 genomes]
rs57704478	1.00[EUR][1000 genomes]
rs58396690	1.00[EUR][1000 genomes]
rs58590469	1.00[EUR][1000 genomes]
rs58849686	1.00[EUR][1000 genomes]
rs58857193	1.00[EUR][1000 genomes]
rs59003501	1.00[EUR][1000 genomes]
rs59614628	1.00[EUR][1000 genomes]
rs59718967	1.00[EUR][1000 genomes]
rs59803839	1.00[EUR][1000 genomes]
rs59810504	1.00[EUR][1000 genomes]
rs59936141	1.00[EUR][1000 genomes]
rs60053855	1.00[EUR][1000 genomes]
rs60234245	1.00[EUR][1000 genomes]
rs60345197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60439721	1.00[EUR][1000 genomes]
rs60484357	1.00[EUR][1000 genomes]
rs60559108	1.00[EUR][1000 genomes]
rs60811448	1.00[EUR][1000 genomes]
rs60857439	1.00[EUR][1000 genomes]
rs60859726	1.00[EUR][1000 genomes]
rs61087655	1.00[EUR][1000 genomes]
rs61211447	1.00[EUR][1000 genomes]
rs61327932	1.00[EUR][1000 genomes]
rs6914753	1.00[EUR][1000 genomes]
rs6915621	1.00[EUR][1000 genomes]
rs6917261	1.00[EUR][1000 genomes]
rs6922109	1.00[EUR][1000 genomes]
rs6922608	1.00[EUR][1000 genomes]
rs6927798	1.00[EUR][1000 genomes]
rs73589002	1.00[EUR][1000 genomes]
rs73591113	1.00[EUR][1000 genomes]
rs73594934	1.00[EUR][1000 genomes]
rs73780508	1.00[EUR][1000 genomes]
rs73780540	1.00[EUR][1000 genomes]
rs7738289	0.89[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7741466	1.00[EUR][1000 genomes]
rs7747486	1.00[EUR][1000 genomes]
rs7751351	1.00[EUR][1000 genomes]
rs7766883	1.00[EUR][1000 genomes]
rs7768531	1.00[EUR][1000 genomes]
rs7773862	1.00[ASN][1000 genomes]
rs7774175	1.00[EUR][1000 genomes]
rs7774376	0.86[CHB][hapmap];1.00[ASN][1000 genomes]
rs7776211	0.89[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9484874	0.89[CHB][hapmap];0.92[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9484875	0.97[ASN][1000 genomes]
rs9496932	1.00[EUR][1000 genomes]
rs9496935	1.00[EUR][1000 genomes]
rs9496938	1.00[EUR][1000 genomes]
rs9496944	1.00[EUR][1000 genomes]
rs9496955	1.00[EUR][1000 genomes]
rs9496962	0.97[ASN][1000 genomes]
rs9496963	0.96[ASN][1000 genomes]
rs9496964	0.89[CHB][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830832	chr6:144572378-144759023	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1031253	chr6:144599055-144883013	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv538461	chr6:144599055-144883013	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1023014	chr6:144717963-144806691	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv527525	chr6:144719765-144737670	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv886739	chr6:144719765-144796516	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144719400-144737000	Weak transcription	Spleen	Spleen
2	chr6:144719600-144744000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:144719800-144743000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr6:144719800-144744400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:144720000-144743200	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr6:144720000-144758200	Weak transcription	Fetal Intestine Small	intestine
7	chr6:144720200-144744000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:144722400-144744000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr6:144723000-144736800	Weak transcription	Right Ventricle	heart
10	chr6:144723200-144736800	Weak transcription	Lung	lung
11	chr6:144723200-144737000	Weak transcription	Right Atrium	heart
12	chr6:144723200-144743000	Weak transcription	Liver	Liver
13	chr6:144726800-144745200	Weak transcription	Fetal Stomach	stomach
14	chr6:144727000-144743000	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr6:144727400-144743000	Weak transcription	Dnd41	blood
16	chr6:144728200-144744400	Weak transcription	Esophagus	oesophagus
17	chr6:144728400-144740000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr6:144728600-144743800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:144729600-144743000	Weak transcription	Fetal Muscle Leg	muscle
20	chr6:144729600-144744000	Weak transcription	Ovary	ovary
21	chr6:144729600-144744400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr6:144729800-144761400	Weak transcription	Colon Smooth Muscle	Colon
23	chr6:144730600-144736600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:144731000-144736800	Weak transcription	Psoas Muscle	Psoas
25	chr6:144731200-144738400	Weak transcription	Small Intestine	intestine
26	chr6:144733000-144736800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr6:144733000-144737600	Weak transcription	HSMMtube	muscle
28	chr6:144733000-144739800	Weak transcription	Primary B cells from peripheral blood	blood
29	chr6:144733000-144742800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr6:144733000-144743000	Weak transcription	GM12878-XiMat	blood
31	chr6:144733000-144744000	Weak transcription	Gastric	stomach
32	chr6:144733200-144736800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr6:144733200-144736800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:144733200-144740000	Weak transcription	Primary T cells from cord blood	blood
35	chr6:144733200-144743000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:144733200-144743000	Weak transcription	Fetal Thymus	thymus
37	chr6:144733200-144744000	Weak transcription	Fetal Lung	lung
38	chr6:144733200-144744000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr6:144733200-144744000	Weak transcription	Thymus	Thymus
40	chr6:144733200-144756800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr6:144733400-144740000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr6:144733400-144740200	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr6:144733400-144744000	Weak transcription	Fetal Kidney	kidney
44	chr6:144733800-144737000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:144734200-144737800	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr6:144734400-144736600	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr6:144734400-144737600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr6:144734400-144737800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr6:144734600-144736600	Weak transcription	NHDF-Ad	bronchial
50	chr6:144734600-144740200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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