Variant report

Variant	rs12660406
Chromosome Location	chr6:144599887-144599888
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	chr6:144597562..144600521-chr6:144605726..144607398,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152818	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs12660513	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12660531	1.00[EUR][1000 genomes]
rs12660596	1.00[EUR][1000 genomes]
rs12661781	1.00[EUR][1000 genomes]
rs12661969	1.00[EUR][1000 genomes]
rs12662267	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12662696	1.00[AMR][1000 genomes];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[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12662914	1.00[AMR][1000 genomes]
rs12663172	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12663380	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12663605	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12663851	1.00[EUR][1000 genomes]
rs12664200	1.00[EUR][1000 genomes]
rs12664245	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12664298	1.00[EUR][1000 genomes]
rs12664304	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12665589	1.00[EUR][1000 genomes]
rs12665850	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17073442	1.00[EUR][1000 genomes]
rs17073463	1.00[EUR][1000 genomes]
rs17073482	1.00[EUR][1000 genomes]
rs17073498	1.00[EUR][1000 genomes]
rs17073506	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	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17073580	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17073598	1.00[EUR][1000 genomes]
rs17073602	1.00[EUR][1000 genomes]
rs17073610	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17073623	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17073629	1.00[EUR][1000 genomes]
rs17073631	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17073672	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17073678	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17840301	1.00[EUR][1000 genomes]
rs1998367	1.00[EUR][1000 genomes]
rs34140249	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34502493	1.00[EUR][1000 genomes]
rs35325795	1.00[EUR][1000 genomes]
rs35681372	1.00[EUR][1000 genomes]
rs36007040	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3811097	1.00[EUR][1000 genomes]
rs4301321	1.00[EUR][1000 genomes]
rs4896714	1.00[EUR][1000 genomes]
rs4896715	1.00[EUR][1000 genomes]
rs4896717	1.00[EUR][1000 genomes]
rs55684976	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56820385	1.00[EUR][1000 genomes]
rs56897751	1.00[EUR][1000 genomes]
rs57069580	1.00[EUR][1000 genomes]
rs57380483	1.00[EUR][1000 genomes]
rs57485302	1.00[EUR][1000 genomes]
rs57592921	1.00[EUR][1000 genomes]
rs57679521	1.00[EUR][1000 genomes]
rs57704478	1.00[EUR][1000 genomes]
rs57712072	1.00[EUR][1000 genomes]
rs57751197	1.00[EUR][1000 genomes]
rs58084770	1.00[EUR][1000 genomes]
rs58396690	1.00[EUR][1000 genomes]
rs58590469	1.00[EUR][1000 genomes]
rs58646546	0.87[AMR][1000 genomes]
rs58847604	1.00[EUR][1000 genomes]
rs58849686	1.00[EUR][1000 genomes]
rs58857193	1.00[EUR][1000 genomes]
rs59003501	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59612420	1.00[EUR][1000 genomes]
rs59614628	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59718967	1.00[EUR][1000 genomes]
rs59803839	1.00[EUR][1000 genomes]
rs59810504	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59892317	1.00[AMR][1000 genomes]
rs59936141	1.00[EUR][1000 genomes]
rs60053855	1.00[EUR][1000 genomes]
rs60188478	1.00[EUR][1000 genomes]
rs60234245	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60345197	1.00[EUR][1000 genomes]
rs60439721	1.00[EUR][1000 genomes]
rs60484357	1.00[EUR][1000 genomes]
rs60559108	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60634096	1.00[EUR][1000 genomes]
rs60661533	1.00[AMR][1000 genomes]
rs60762289	1.00[EUR][1000 genomes]
rs60811448	1.00[EUR][1000 genomes]
rs60857439	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60859726	1.00[EUR][1000 genomes]
rs61087655	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61211447	1.00[EUR][1000 genomes]
rs61249035	1.00[EUR][1000 genomes]
rs61327932	1.00[AMR][1000 genomes];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]
rs7741466	1.00[EUR][1000 genomes]
rs7745240	1.00[EUR][1000 genomes]
rs7747486	1.00[EUR][1000 genomes]
rs7751351	1.00[EUR][1000 genomes]
rs7751876	1.00[EUR][1000 genomes]
rs7754883	1.00[EUR][1000 genomes]
rs7766883	1.00[EUR][1000 genomes]
rs7768531	1.00[EUR][1000 genomes]
rs7774175	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9484874	1.00[EUR][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]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830831	chr6:144501371-144649509	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	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
3	esv2422260	chr6:144574591-144731630	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	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
5	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

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144587800-144605000	Weak transcription	Right Atrium	heart
2	chr6:144587800-144605800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:144598400-144600400	Enhancers	Liver	Liver
4	chr6:144598600-144600400	Enhancers	Adipose Nuclei	Adipose
5	chr6:144599200-144600000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:144599200-144600400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:144599200-144600400	Enhancers	NHEK	skin
8	chr6:144599200-144600600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:144599200-144601000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:144599200-144605000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:144599600-144600200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:144599600-144600400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:144599600-144600400	Enhancers	Hela-S3	cervix
14	chr6:144599600-144600800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:144599600-144601000	Enhancers	HMEC	breast
16	chr6:144599600-144601400	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr6:144599600-144601400	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr6:144599600-144601600	Enhancers	H9 Cell Line	embryonic stem cell
19	chr6:144599800-144600000	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr6:144599800-144600200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr6:144599800-144600200	Enhancers	Placenta	Placenta
22	chr6:144599800-144600200	Enhancers	Pancreas	Pancrea
23	chr6:144599800-144600200	Enhancers	Placenta Amnion	Placenta Amnion
24	chr6:144599800-144600200	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr6:144599800-144600200	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr6:144599800-144600200	Enhancers	A549	lung
27	chr6:144599800-144600400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr6:144599800-144600400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:144599800-144600600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr6:144599800-144600800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr6:144599800-144601200	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr6:144599800-144601200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:144599800-144601200	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr6:144599800-144601200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr6:144599800-144601400	Enhancers	H1 Cell Line	embryonic stem cell
36	chr6:144599800-144601400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links