Variant report

Variant	rs12661969
Chromosome Location	chr6:144672674-144672675
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	chr6:144671254..144672966-chr6:144680487..144682454,2	MCF-7	breast:

Extended variants
information (count: 119 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs12660406	1.00[EUR][1000 genomes]
rs12660513	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs12660531	1.00[EUR][1000 genomes]
rs12660596	1.00[EUR][1000 genomes]
rs12661781	1.00[EUR][1000 genomes]
rs12662267	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][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	0.84[CHB][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12663605	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs12663851	1.00[EUR][1000 genomes]
rs12664200	1.00[EUR][1000 genomes]
rs12664245	1.00[EUR][1000 genomes]
rs12664298	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs12664304	1.00[EUR][1000 genomes]
rs12665589	1.00[EUR][1000 genomes]
rs12665850	0.84[CHB][hapmap];1.00[EUR][1000 genomes];0.87[ASN][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	1.00[EUR][1000 genomes]
rs17073580	1.00[EUR][1000 genomes]
rs17073598	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs17073602	1.00[EUR][1000 genomes]
rs17073610	1.00[EUR][1000 genomes]
rs17073623	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs17073629	1.00[MEX][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17073631	1.00[EUR][1000 genomes]
rs17073672	0.84[CHB][hapmap];1.00[EUR][1000 genomes];0.86[ASN][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];0.87[ASN][1000 genomes]
rs34502493	1.00[EUR][1000 genomes]
rs35325795	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36007040	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	1.00[EUR][1000 genomes]
rs56820385	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]
rs58396690	1.00[EUR][1000 genomes]
rs58590469	1.00[EUR][1000 genomes]
rs58646546	0.87[ASN][1000 genomes]
rs58847604	1.00[EUR][1000 genomes]
rs58849686	1.00[EUR][1000 genomes]
rs58857193	1.00[EUR][1000 genomes]
rs59003501	1.00[EUR][1000 genomes]
rs59612420	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];0.99[ASN][1000 genomes]
rs59892317	1.00[ASN][1000 genomes]
rs59936141	1.00[EUR][1000 genomes]
rs60053855	1.00[EUR][1000 genomes]
rs60188478	1.00[EUR][1000 genomes]
rs60234245	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[EUR][1000 genomes]
rs60634096	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	0.92[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6922109	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6922608	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6927798	1.00[EUR][1000 genomes]
rs73589002	1.00[EUR][1000 genomes]
rs73591113	1.00[EUR][1000 genomes]
rs73592848	0.99[AFR][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]
rs7747486	1.00[EUR][1000 genomes]
rs7748561	0.99[AFR][1000 genomes]
rs7751351	1.00[EUR][1000 genomes]
rs7751876	1.00[EUR][1000 genomes]
rs7766883	1.00[EUR][1000 genomes]
rs7768531	1.00[EUR][1000 genomes]
rs7774175	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9484874	1.00[EUR][1000 genomes]
rs9496932	1.00[EUR][1000 genomes]
rs9496935	0.84[CHB][hapmap];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9496938	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9496944	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496955	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	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:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144648800-144672800	Weak transcription	Fetal Stomach	stomach
2	chr6:144653200-144684600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:144663200-144685800	Weak transcription	Brain Substantia Nigra	brain
4	chr6:144663400-144675200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:144665400-144696400	Weak transcription	Fetal Intestine Small	intestine
6	chr6:144667600-144674800	Enhancers	Primary B cells from peripheral blood	blood
7	chr6:144668800-144673000	Weak transcription	Brain Angular Gyrus	brain
8	chr6:144668800-144673000	Weak transcription	Placenta	Placenta
9	chr6:144668800-144681600	Weak transcription	Small Intestine	intestine
10	chr6:144669400-144673000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr6:144670400-144673400	Flanking Active TSS	HUVEC	blood vessel
12	chr6:144670400-144674000	Flanking Active TSS	Dnd41	blood
13	chr6:144670400-144674200	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr6:144670400-144674200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr6:144670600-144672800	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr6:144670600-144673200	Genic enhancers	HepG2	liver
17	chr6:144670800-144672800	Enhancers	Stomach Smooth Muscle	stomach
18	chr6:144670800-144673200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:144670800-144673400	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr6:144670800-144673400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr6:144670800-144673400	Enhancers	Fetal Heart	heart
22	chr6:144670800-144673600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr6:144670800-144673800	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr6:144670800-144673800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
25	chr6:144670800-144673800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:144670800-144674200	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr6:144670800-144691200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:144671000-144672800	Weak transcription	Lung	lung
29	chr6:144671000-144672800	Enhancers	Rectal Smooth Muscle	rectum
30	chr6:144671000-144673000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:144671000-144673000	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr6:144671000-144681600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:144671000-144683200	Weak transcription	Gastric	stomach
34	chr6:144671200-144672800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr6:144671200-144673000	Weak transcription	Fetal Lung	lung
36	chr6:144671200-144673000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr6:144671200-144673600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr6:144671200-144674800	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr6:144671200-144675200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr6:144671200-144692000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr6:144671400-144672800	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr6:144671400-144672800	Weak transcription	Right Atrium	heart
43	chr6:144671400-144673000	Enhancers	Brain Anterior Caudate	brain
44	chr6:144671400-144675200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr6:144671400-144675400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr6:144671400-144681600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr6:144671400-144681600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr6:144671600-144673600	Weak transcription	Fetal Kidney	kidney
49	chr6:144671600-144675400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr6:144671800-144672800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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