Variant report

Variant	rs10877925
Chromosome Location	chr12:63292357-63292358
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:63273431..63275241-chr12:63290276..63292669,2	MCF-7	breast:
2	chr12:63291380..63293253-chr12:63327047..63329993,2	MCF-7	breast:
3	chr12:63284474..63287928-chr12:63291672..63294715,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111110	Chromatin interaction
ENSG00000252660	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10784318	0.87[CHB][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.80[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1081782	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877923	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877924	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11174712	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1545897	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3847908	0.86[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs486118	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs489033	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs524688	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs699570	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs699572	0.83[ASN][1000 genomes]
rs699573	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]
rs699576	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs808868	0.87[CHB][hapmap];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:42 , 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	chr12:63286200-63293600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:63286400-63293400	Weak transcription	A549	lung
7	chr12:63287400-63293000	Weak transcription	Stomach Mucosa	stomach
8	chr12:63287400-63309000	Weak transcription	Pancreas	Pancrea
9	chr12:63287800-63316400	Weak transcription	Fetal Intestine Small	intestine
10	chr12:63289400-63293000	Weak transcription	Placenta	Placenta
11	chr12:63289400-63293400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:63289600-63293400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr12:63289600-63293800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:63289600-63294600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:63289600-63294600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:63289600-63294600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:63289600-63306600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr12:63289800-63294600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr12:63289800-63294800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:63291200-63294200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr12:63291400-63292800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr12:63291400-63293400	Enhancers	HepG2	liver
23	chr12:63291400-63295000	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr12:63291400-63295600	Enhancers	Brain Angular Gyrus	brain
25	chr12:63291400-63295600	Enhancers	Brain Anterior Caudate	brain
26	chr12:63291400-63297400	Enhancers	Brain Substantia Nigra	brain
27	chr12:63291600-63292600	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr12:63291600-63294200	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr12:63291600-63295000	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr12:63291600-63295200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:63291600-63295600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:63291600-63295600	Enhancers	Brain Hippocampus Middle	brain
33	chr12:63291600-63295800	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr12:63291800-63292600	Weak transcription	Right Ventricle	heart
35	chr12:63291800-63292800	Enhancers	Primary hematopoietic stem cells	blood
36	chr12:63291800-63295600	Enhancers	Brain Cingulate Gyrus	brain
37	chr12:63292000-63292400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:63292000-63293600	Weak transcription	K562	blood
39	chr12:63292000-63295800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:63292200-63292600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:63292200-63292800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr12:63292200-63293000	Enhancers	Muscle Satellite Cultured Cells	--

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