Variant report

Variant	rs12662565
Chromosome Location	chr6:76510233-76510234
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:76458151..76460204-chr6:76508738..76510333,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196586	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs11963710	0.90[ASN][1000 genomes]
rs11964201	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11967411	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11968058	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11968226	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11969264	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12660075	0.91[ASN][1000 genomes]
rs12660330	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12660493	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12661973	0.86[ASN][1000 genomes]
rs12662248	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12662475	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12662672	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12662718	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12662824	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12662879	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12663203	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12663535	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12664146	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12664721	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12664742	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12665404	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13205059	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16879451	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2273858	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2295937	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3778009	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3798436	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3798445	0.97[ASN][1000 genomes]
rs3798450	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798451	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798452	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3798453	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3798456	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3798457	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56251027	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59710688	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60360183	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61620194	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67182025	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72654751	0.86[ASN][1000 genomes]
rs72654752	0.89[ASN][1000 genomes]
rs72654753	0.91[ASN][1000 genomes]
rs72654754	0.91[ASN][1000 genomes]
rs72654755	0.90[ASN][1000 genomes]
rs72654756	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72654757	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72654758	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72654759	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72654760	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72654761	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72654762	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72654763	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72654764	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72654765	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72654766	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72654767	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72654769	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72654770	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72654771	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72654772	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72654773	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72654774	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72654775	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72654776	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72654777	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72654778	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72654779	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72654780	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72654781	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72654783	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72654784	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72654785	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72654786	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72654787	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72654788	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72654789	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72654790	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72654791	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72654792	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72654793	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72674543	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72674544	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72674546	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73751021	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73751022	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73751024	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7761217	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9443187	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9443191	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9443192	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9447543	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9447544	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9447545	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9447546	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9447549	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9447552	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9447555	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022428	chr6:76023118-76575620	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv538312	chr6:76023118-76575620	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
3	nsv1032245	chr6:76045537-76545703	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
4	nsv538313	chr6:76045537-76545703	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
5	nsv1019328	chr6:76154751-76604197	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
6	nsv538314	chr6:76154751-76604197	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
7	nsv1017542	chr6:76238459-76537447	Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
8	nsv1021090	chr6:76306100-76759397	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
9	nsv538318	chr6:76306100-76759397	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
10	nsv1032961	chr6:76343575-76788852	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	nsv932201	chr6:76365548-77219650	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv1028340	chr6:76410921-76960225	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
13	nsv538319	chr6:76410921-76960225	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
14	nsv933055	chr6:76493217-76515893	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:76472600-76528000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr6:76485400-76523000	Weak transcription	Lung	lung
3	chr6:76491200-76523000	Weak transcription	Fetal Intestine Large	intestine
4	chr6:76492400-76523000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:76497000-76514000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:76501800-76540800	Weak transcription	Left Ventricle	heart
7	chr6:76502600-76527400	Weak transcription	HUVEC	blood vessel
8	chr6:76504200-76522400	Weak transcription	Fetal Kidney	kidney
9	chr6:76505000-76522400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:76505200-76527200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:76505400-76521800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:76505600-76523000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:76505800-76513800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:76506000-76523200	Weak transcription	Brain Anterior Caudate	brain
15	chr6:76506200-76516600	Weak transcription	Brain Hippocampus Middle	brain
16	chr6:76507200-76523000	Weak transcription	Fetal Stomach	stomach
17	chr6:76507600-76521800	Weak transcription	Fetal Intestine Small	intestine
18	chr6:76509400-76510600	Enhancers	H1 Cell Line	embryonic stem cell
19	chr6:76509400-76510600	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr6:76509400-76511200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr6:76509600-76511000	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr6:76509600-76528000	Weak transcription	NH-A	brain
23	chr6:76509800-76510400	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr6:76509800-76511400	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr6:76510000-76511200	Enhancers	iPS-20b Cell Line	embryonic stem cell

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