Variant report

Variant	rs12519552
Chromosome Location	chr5:106910910-106910911
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	chr5:106906707..106911009-chr5:107006315..107009316,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184349	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10043284	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10043302	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10044934	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515374	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12110095	1.00[ASN][1000 genomes]
rs12514246	1.00[ASN][1000 genomes]
rs12515248	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12519591	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12520660	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12522223	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17160227	0.93[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58880008	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58882389	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6881619	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6888194	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6895165	0.93[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6897852	1.00[JPT][hapmap]
rs6898202	1.00[JPT][hapmap]
rs755966	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7726649	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7732162	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9328006	0.86[CEU][hapmap];0.90[GIH][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs957662	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9986282	1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034276	chr5:106461538-106944163	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv537851	chr5:106461538-106944163	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv34018	chr5:106720912-107110506	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106899400-106915600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:106907800-106912800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:106907800-106913400	Weak transcription	Right Ventricle	heart
4	chr5:106907800-106914000	Enhancers	Fetal Heart	heart
5	chr5:106908000-106911600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr5:106908200-106911800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr5:106908200-106912600	Weak transcription	Placenta	Placenta
8	chr5:106908200-106913800	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr5:106908200-106916600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:106908400-106913800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr5:106908600-106911400	Weak transcription	HUVEC	blood vessel
12	chr5:106908600-106912000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr5:106908600-106912000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:106908600-106913200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr5:106908800-106911000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:106908800-106911000	Weak transcription	GM12878-XiMat	blood
17	chr5:106908800-106911400	Weak transcription	Fetal Kidney	kidney
18	chr5:106908800-106912400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr5:106908800-106912600	Weak transcription	Fetal Stomach	stomach
20	chr5:106908800-106917000	Weak transcription	HSMM	muscle
21	chr5:106908800-106917600	Enhancers	A549	lung
22	chr5:106909000-106911000	Enhancers	Fetal Lung	lung
23	chr5:106909000-106911600	Weak transcription	HMEC	breast
24	chr5:106909000-106911800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr5:106909000-106911800	Weak transcription	NHEK	skin
26	chr5:106909000-106912000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:106909000-106912200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:106909000-106912200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr5:106909000-106912400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:106909000-106912800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:106909000-106912800	Weak transcription	Right Atrium	heart
32	chr5:106909000-106913200	Weak transcription	Fetal Muscle Leg	muscle
33	chr5:106909000-106913800	Weak transcription	NHDF-Ad	bronchial
34	chr5:106909000-106914000	Weak transcription	Left Ventricle	heart
35	chr5:106909000-106914400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr5:106909000-106917000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr5:106909400-106911400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr5:106909600-106912000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr5:106909600-106913800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr5:106910000-106911400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr5:106910200-106912600	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr5:106910200-106914000	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr5:106910400-106911000	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr5:106910400-106914000	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr5:106910600-106911000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr5:106910600-106911800	Weak transcription	Adipose Nuclei	Adipose
47	chr5:106910800-106911000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr5:106910800-106911800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr5:106910800-106912800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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