Variant report

Variant	rs12668460
Chromosome Location	chr7:111719459-111719460
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	chr7:111718019..111719728-chr7:111726986..111728960,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1012804	0.95[ASN][1000 genomes]
rs1012806	0.94[ASN][1000 genomes]
rs10225837	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10236078	0.92[ASN][1000 genomes]
rs10256513	0.99[ASN][1000 genomes]
rs10261464	0.94[ASN][1000 genomes]
rs10262170	0.88[ASN][1000 genomes]
rs10266032	0.96[ASN][1000 genomes]
rs10281256	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10487338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11971933	0.94[ASN][1000 genomes]
rs11973245	0.88[ASN][1000 genomes]
rs11977671	0.96[ASN][1000 genomes]
rs12665946	0.92[ASN][1000 genomes]
rs12666013	0.94[ASN][1000 genomes]
rs12668526	0.92[ASN][1000 genomes]
rs1593871	0.91[ASN][1000 genomes]
rs2106912	0.92[ASN][1000 genomes]
rs28562311	0.97[ASN][1000 genomes]
rs2894634	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4730509	0.92[ASN][1000 genomes]
rs58092763	0.94[ASN][1000 genomes]
rs6944979	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6948142	0.93[ASN][1000 genomes]
rs6953244	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6958405	0.94[ASN][1000 genomes]
rs6958532	0.83[ASN][1000 genomes]
rs6959338	0.95[ASN][1000 genomes]
rs6962255	0.83[ASN][1000 genomes]
rs72603556	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs72603557	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs769082	0.90[ASN][1000 genomes]
rs769083	0.90[ASN][1000 genomes]
rs769084	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7791324	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7796169	0.86[ASN][1000 genomes]
rs7800386	0.93[ASN][1000 genomes]
rs7802825	0.92[ASN][1000 genomes]
rs7802845	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[ASN][1000 genomes]
rs7808571	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9770487	0.83[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	nsv608196	chr7:111073710-111794368	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv1021527	chr7:111194596-111851619	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv539086	chr7:111194596-111851619	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv539088	chr7:111333899-111722341	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv531435	chr7:111333900-111926292	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv491934	chr7:111333900-111975504	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv532335	chr7:111411990-112054905	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv533924	chr7:111529515-111784369	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
9	nsv1023261	chr7:111593889-111780337	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
10	nsv1016663	chr7:111622107-111813223	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv1034249	chr7:111656902-111748774	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv539089	chr7:111656902-111748774	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv889054	chr7:111666943-111739842	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	esv1844097	chr7:111686153-111723488	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	2 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	chr7:111711200-111720600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr7:111712600-111719600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr7:111712800-111719600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr7:111713000-111723800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr7:111713200-111720600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr7:111713200-111724000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr7:111713200-111742400	Weak transcription	Right Ventricle	heart
8	chr7:111715000-111720600	Weak transcription	Aorta	Aorta
9	chr7:111715000-111721000	Weak transcription	Lung	lung
10	chr7:111715200-111726600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr7:111715600-111719600	Weak transcription	HUVEC	blood vessel
12	chr7:111715800-111719800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr7:111716000-111720600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr7:111717000-111719600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr7:111717000-111720600	Weak transcription	NHLF	lung
16	chr7:111717000-111720800	Weak transcription	Adipose Nuclei	Adipose
17	chr7:111717400-111719800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr7:111717800-111723800	Weak transcription	Brain Angular Gyrus	brain
19	chr7:111718400-111719600	Enhancers	A549	lung
20	chr7:111718600-111721600	Enhancers	Fetal Lung	lung
21	chr7:111718600-111721800	Enhancers	Liver	Liver
22	chr7:111718800-111720600	Weak transcription	Brain Anterior Caudate	brain
23	chr7:111718800-111721000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr7:111719200-111719800	Enhancers	Colon Smooth Muscle	Colon
25	chr7:111719200-111721000	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr7:111719200-111721000	Enhancers	Brain Substantia Nigra	brain
27	chr7:111719200-111721000	Enhancers	HepG2	liver
28	chr7:111719200-111721400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr7:111719200-111721400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr7:111719200-111721600	Enhancers	Hela-S3	cervix
31	chr7:111719400-111719800	Enhancers	Brain Hippocampus Middle	brain
32	chr7:111719400-111720000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr7:111719400-111720000	Enhancers	HMEC	breast
34	chr7:111719400-111720200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr7:111719400-111720800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr7:111719400-111721400	Enhancers	NHEK	skin

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