Variant report

Variant	rs641406
Chromosome Location	chr5:106914027-106914028
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	chr5:106911881..106914239-chr5:106916867..106919606,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs10061771	0.87[CHD][hapmap]
rs103840	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12153493	1.00[CHB][hapmap]
rs1990993	0.87[CHD][hapmap]
rs2005103	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3864269	0.87[CHD][hapmap]
rs4957704	0.87[CHD][hapmap]
rs591470	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs607976	1.00[CEU][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs685820	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6888055	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7734574	0.89[GIH][hapmap];0.81[MEX][hapmap]
rs7737882	0.89[GIH][hapmap];0.86[MEX][hapmap]
rs872240	1.00[ASW][hapmap];0.82[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9328010	0.82[CEU][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9686509	0.89[GIH][hapmap];0.86[MEX][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:45 , 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	chr5:106908200-106916600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr5:106908800-106917000	Weak transcription	HSMM	muscle
4	chr5:106908800-106917600	Enhancers	A549	lung
5	chr5:106909000-106914400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:106909000-106917000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr5:106911000-106914200	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr5:106911000-106914400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:106911000-106914800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr5:106911400-106914200	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr5:106911400-106915200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:106911400-106915600	Enhancers	Fetal Lung	lung
13	chr5:106911600-106914600	Enhancers	HMEC	breast
14	chr5:106911800-106914800	Enhancers	NHEK	skin
15	chr5:106911800-106915000	Enhancers	Adipose Nuclei	Adipose
16	chr5:106912000-106914600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:106912000-106914600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:106912200-106916600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr5:106912200-106917600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:106912800-106914600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:106913400-106914200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:106913400-106915000	Enhancers	GM12878-XiMat	blood
23	chr5:106913400-106916800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:106913600-106914600	Weak transcription	Fetal Kidney	kidney
25	chr5:106913600-106914800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr5:106913600-106916800	Weak transcription	Fetal Muscle Leg	muscle
27	chr5:106913600-106917000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr5:106913600-106917200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr5:106913600-106928800	Weak transcription	Right Ventricle	heart
30	chr5:106913800-106914600	Enhancers	Muscle Satellite Cultured Cells	--
31	chr5:106913800-106914600	Enhancers	Osteobl	bone
32	chr5:106913800-106915000	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr5:106913800-106915000	Enhancers	NHDF-Ad	bronchial
34	chr5:106913800-106916600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr5:106913800-106916800	Weak transcription	Fetal Stomach	stomach
36	chr5:106913800-106917000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr5:106913800-106924000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr5:106914000-106914200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr5:106914000-106914200	Enhancers	Left Ventricle	heart
40	chr5:106914000-106916600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr5:106914000-106916800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr5:106914000-106916800	Weak transcription	Fetal Heart	heart
43	chr5:106914000-106917000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr5:106914000-106917200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr5:106914000-106924800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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