Variant report

Variant	rs163890
Chromosome Location	chr5:106876402-106876403
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	chr5:106867857..106870035-chr5:106875652..106879640,3	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1471041	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs149155	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs163614	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs163889	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs163891	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs163893	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs164697	0.90[ASN][1000 genomes]
rs164850	0.90[ASN][1000 genomes]
rs164851	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs164971	0.90[ASN][1000 genomes]
rs341276	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs341277	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs341278	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs352612	0.90[ASN][1000 genomes]
rs352613	0.90[ASN][1000 genomes]
rs395904	0.90[ASN][1000 genomes]
rs39918	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs458393	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs462885	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs464250	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs57889678	0.89[ASN][1000 genomes]
rs58772568	0.89[ASN][1000 genomes]
rs59747234	0.89[ASN][1000 genomes]
rs60575744	1.00[ASN][1000 genomes]
rs61200118	0.89[ASN][1000 genomes]
rs61415460	0.89[ASN][1000 genomes]
rs698372	0.87[EUR][1000 genomes]
rs848829	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs849520	1.00[JPT][hapmap];1.00[ASN][1000 genomes]

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:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106842400-106880000	Weak transcription	Gastric	stomach
2	chr5:106865400-106880000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:106867200-106879800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:106868800-106877400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr5:106868800-106878000	Weak transcription	Right Atrium	heart
6	chr5:106871000-106878200	Weak transcription	Fetal Lung	lung
7	chr5:106872000-106877800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr5:106872200-106878200	Weak transcription	Pancreas	Pancrea
9	chr5:106872400-106877800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:106873600-106882600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:106873800-106877200	Weak transcription	Stomach Mucosa	stomach
12	chr5:106874000-106876600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:106874200-106877200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:106874600-106877200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:106874600-106877400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:106874600-106877400	Weak transcription	NHEK	skin
17	chr5:106874800-106877200	Weak transcription	HMEC	breast
18	chr5:106874800-106877800	Weak transcription	NH-A	brain
19	chr5:106874800-106878000	Weak transcription	HSMMtube	muscle
20	chr5:106875000-106877000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr5:106875000-106877200	Weak transcription	HSMM	muscle
22	chr5:106875000-106877800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr5:106875000-106877800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr5:106875000-106878000	Weak transcription	Right Ventricle	heart
25	chr5:106875000-106882800	Weak transcription	Brain Angular Gyrus	brain
26	chr5:106875000-106885200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr5:106875200-106877200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr5:106875200-106877200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr5:106875200-106878000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:106875200-106878000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr5:106875200-106878000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:106875200-106878000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr5:106875200-106878000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr5:106875200-106878000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr5:106875200-106878200	Weak transcription	Psoas Muscle	Psoas
36	chr5:106875400-106878200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr5:106875600-106877600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr5:106875800-106877200	Weak transcription	Colon Smooth Muscle	Colon
39	chr5:106875800-106877200	Weak transcription	NHDF-Ad	bronchial
40	chr5:106875800-106878200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr5:106875800-106878200	Weak transcription	Fetal Muscle Leg	muscle
42	chr5:106875800-106878200	Weak transcription	Thymus	Thymus
43	chr5:106875800-106878600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr5:106875800-106879000	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr5:106875800-106879600	Weak transcription	Esophagus	oesophagus
46	chr5:106875800-106879600	Weak transcription	Left Ventricle	heart
47	chr5:106876000-106877000	Weak transcription	GM12878-XiMat	blood
48	chr5:106876000-106877400	Weak transcription	Fetal Heart	heart
49	chr5:106876000-106877800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr5:106876000-106877800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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