Variant report

Variant	rs12662914
Chromosome Location	chr6:144645433-144645434
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:144642782..144645607-chr6:144652878..144655229,2	MCF-7	breast:
2	chr6:144641871..144646816-chr6:144650336..144652619,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225311	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs11962764	0.91[JPT][hapmap]
rs12660406	1.00[AMR][1000 genomes]
rs12660513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12662267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12662696	0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12662872	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12662904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12663172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12663380	0.87[AMR][1000 genomes]
rs12663605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12664245	1.00[AMR][1000 genomes]
rs12664304	0.94[JPT][hapmap];1.00[AMR][1000 genomes]
rs12665850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1474630	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs17073442	1.00[AFR][1000 genomes]
rs17073463	1.00[AFR][1000 genomes]
rs17073482	1.00[AFR][1000 genomes]
rs17073506	1.00[AFR][1000 genomes]
rs17073509	1.00[AFR][1000 genomes]
rs17073524	1.00[AFR][1000 genomes]
rs17073528	1.00[AFR][1000 genomes]
rs17073529	1.00[AFR][1000 genomes]
rs17073539	1.00[AFR][1000 genomes]
rs17073544	1.00[AFR][1000 genomes]
rs17073571	0.87[JPT][hapmap];0.87[AMR][1000 genomes]
rs17073578	0.93[JPT][hapmap]
rs17073580	0.87[JPT][hapmap];0.87[AMR][1000 genomes]
rs17073596	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs17073598	0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs17073602	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs17073610	0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17073623	0.93[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17073629	0.80[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17073631	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17073672	1.00[AMR][1000 genomes]
rs17073678	0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17840301	1.00[AFR][1000 genomes]
rs1998367	1.00[AFR][1000 genomes]
rs34140249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34502493	1.00[AFR][1000 genomes]
rs34643516	1.00[AFR][1000 genomes]
rs36007040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs55684976	0.87[AMR][1000 genomes]
rs57380483	1.00[AFR][1000 genomes]
rs57485302	1.00[AFR][1000 genomes]
rs57592921	1.00[AFR][1000 genomes]
rs57704478	1.00[AFR][1000 genomes]
rs57751197	1.00[AFR][1000 genomes]
rs58396690	1.00[AFR][1000 genomes]
rs58590469	1.00[AFR][1000 genomes]
rs58646546	0.87[AMR][1000 genomes]
rs58847604	1.00[AFR][1000 genomes]
rs58849686	1.00[AFR][1000 genomes]
rs58857193	1.00[AFR][1000 genomes]
rs58981502	1.00[AFR][1000 genomes]
rs59003501	1.00[AMR][1000 genomes]
rs59612420	1.00[AFR][1000 genomes]
rs59614628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59718967	1.00[ASN][1000 genomes]
rs59803839	0.89[ASN][1000 genomes]
rs59810504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59892317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59936141	1.00[AFR][1000 genomes]
rs60053855	1.00[AFR][1000 genomes]
rs60188478	1.00[AFR][1000 genomes]
rs60234245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60439721	1.00[AFR][1000 genomes]
rs60484357	1.00[AFR][1000 genomes]
rs60559108	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60661533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs60811448	1.00[AFR][1000 genomes]
rs60857439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs60859726	0.81[ASN][1000 genomes]
rs61087655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs61211447	1.00[AFR][1000 genomes]
rs61327932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6903169	0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs6911171	0.98[ASN][1000 genomes]
rs6916795	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6919115	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6924797	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6927798	0.93[JPT][hapmap]
rs6941296	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs73588920	0.96[ASN][1000 genomes]
rs73589002	1.00[ASN][1000 genomes]
rs73591113	0.98[ASN][1000 genomes]
rs73780508	0.83[ASN][1000 genomes]
rs7741466	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7745998	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7768531	0.93[JPT][hapmap]
rs7774175	0.87[AMR][1000 genomes]
rs9321968	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9321969	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9496925	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9496928	0.98[ASN][1000 genomes]
rs9496930	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][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:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144616400-144648000	Weak transcription	NHEK	skin
2	chr6:144624400-144648000	Weak transcription	HMEC	breast
3	chr6:144627600-144645800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:144630200-144648400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:144630600-144648200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:144635000-144651000	Weak transcription	Small Intestine	intestine
7	chr6:144635600-144650800	Weak transcription	Aorta	Aorta
8	chr6:144636000-144656200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:144636600-144648000	Weak transcription	Brain Anterior Caudate	brain
10	chr6:144636600-144654800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:144636800-144650800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr6:144636800-144654800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr6:144636800-144656400	Weak transcription	Brain Substantia Nigra	brain
14	chr6:144637000-144647600	Weak transcription	Fetal Muscle Leg	muscle
15	chr6:144637000-144651800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr6:144637200-144647800	Weak transcription	Left Ventricle	heart
17	chr6:144637200-144647800	Weak transcription	Right Atrium	heart
18	chr6:144637200-144648000	Weak transcription	Psoas Muscle	Psoas
19	chr6:144637400-144645600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:144637400-144647800	Weak transcription	Fetal Stomach	stomach
21	chr6:144637400-144648400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr6:144637600-144647800	Weak transcription	Right Ventricle	heart
23	chr6:144639600-144660200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:144641000-144645600	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr6:144641200-144645600	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr6:144641200-144648000	Weak transcription	Lung	lung
27	chr6:144642200-144646200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr6:144642200-144646400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:144642200-144647600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:144642200-144647600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr6:144642200-144654800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr6:144642200-144655200	Weak transcription	Thymus	Thymus
33	chr6:144642200-144659800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:144642400-144645600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr6:144642400-144646000	Weak transcription	Adipose Nuclei	Adipose
36	chr6:144642600-144647200	Weak transcription	Fetal Heart	heart
37	chr6:144642600-144648000	Weak transcription	Fetal Lung	lung
38	chr6:144642600-144649200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr6:144643000-144646600	Enhancers	Stomach Mucosa	stomach
40	chr6:144643200-144651600	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr6:144643600-144645600	Weak transcription	NH-A	brain
42	chr6:144643600-144646200	Weak transcription	Pancreas	Pancrea
43	chr6:144643600-144648000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr6:144643600-144648000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr6:144643600-144648000	Weak transcription	Gastric	stomach
46	chr6:144643600-144648000	Weak transcription	NHLF	lung
47	chr6:144643600-144648200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:144643600-144651200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr6:144643600-144652600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr6:144643600-144656400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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