Variant report

Variant	rs699573
Chromosome Location	chr12:63291364-63291365
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	chr12:63273431..63275241-chr12:63290276..63292669,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10784318	0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1081782	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10877923	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877924	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10877925	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11174712	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1545897	0.91[CEU][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3847908	0.86[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs486118	0.92[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs489033	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs524688	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs699570	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs699572	0.95[ASN][1000 genomes]
rs699576	0.83[CHB][hapmap];0.87[MEX][hapmap]
rs808868	0.87[CHB][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs867393	0.82[JPT][hapmap]

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	esv3415227	chr12:63228121-63591615	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv899161	chr12:63275017-63311148	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv899162	chr12:63279750-63334242	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
4	nsv899163	chr12:63288343-63325988	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:63271600-63294400	Weak transcription	Ovary	ovary
2	chr12:63281000-63293000	Weak transcription	Left Ventricle	heart
3	chr12:63281200-63293600	Weak transcription	Gastric	stomach
4	chr12:63282200-63295400	Weak transcription	Lung	lung
5	chr12:63284200-63291400	Weak transcription	Brain Angular Gyrus	brain
6	chr12:63285600-63291400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:63286200-63291400	Weak transcription	Brain Anterior Caudate	brain
8	chr12:63286200-63291600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr12:63286200-63293600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:63286400-63291400	Weak transcription	Brain Substantia Nigra	brain
11	chr12:63286400-63291600	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr12:63286400-63291600	Weak transcription	Brain Hippocampus Middle	brain
13	chr12:63286400-63293400	Weak transcription	A549	lung
14	chr12:63286800-63291800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:63286800-63291800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr12:63287400-63293000	Weak transcription	Stomach Mucosa	stomach
17	chr12:63287400-63309000	Weak transcription	Pancreas	Pancrea
18	chr12:63287600-63291400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:63287600-63291600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:63287600-63292000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:63287800-63316400	Weak transcription	Fetal Intestine Small	intestine
22	chr12:63289400-63293000	Weak transcription	Placenta	Placenta
23	chr12:63289400-63293400	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr12:63289600-63293400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr12:63289600-63293800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr12:63289600-63294600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr12:63289600-63294600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr12:63289600-63294600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr12:63289600-63306600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr12:63289800-63294600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr12:63289800-63294800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:63290000-63291400	Weak transcription	HepG2	liver
33	chr12:63291200-63294200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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