Variant report

Variant	rs662627
Chromosome Location	chr5:106881333-106881334
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	chr5:106879004..106882642-chr5:106901897..106905418,3	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs163727	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs164699	0.81[CHB][hapmap]
rs164844	0.82[CHB][hapmap]
rs2161514	0.91[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2445074	0.86[CHB][hapmap]
rs2457867	0.90[ASN][1000 genomes]
rs2484103	0.91[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.86[ASN][1000 genomes]
rs341272	0.86[CHB][hapmap]
rs341274	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs342603	0.95[CHB][hapmap]
rs342604	0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs352609	0.91[CHB][hapmap]
rs41375	0.95[CHB][hapmap]
rs445747	0.95[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs459400	0.95[CHB][hapmap]
rs459637	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs464950	0.95[CHB][hapmap]
rs467089	0.95[CHB][hapmap]
rs553363	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs555989	0.90[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs677797	0.86[CHB][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:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106873600-106882600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:106875000-106882800	Weak transcription	Brain Angular Gyrus	brain
3	chr5:106875000-106885200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:106877400-106883400	Enhancers	Fetal Heart	heart
5	chr5:106877800-106881400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:106878200-106883200	Enhancers	Fetal Lung	lung
7	chr5:106878400-106882600	Weak transcription	Dnd41	blood
8	chr5:106878600-106881600	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr5:106878600-106881600	Enhancers	Stomach Mucosa	stomach
10	chr5:106878600-106882000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:106878800-106891600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:106879000-106882800	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr5:106879000-106882800	Weak transcription	Thymus	Thymus
14	chr5:106879000-106884400	Weak transcription	HSMMtube	muscle
15	chr5:106879000-106884400	Weak transcription	NHDF-Ad	bronchial
16	chr5:106879000-106893000	Weak transcription	Psoas Muscle	Psoas
17	chr5:106879000-106899200	Weak transcription	Fetal Stomach	stomach
18	chr5:106879200-106884200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:106879400-106881400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr5:106879400-106884400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr5:106879400-106888200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:106879400-106888800	Weak transcription	HMEC	breast
23	chr5:106879600-106888000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr5:106879800-106881600	Enhancers	A549	lung
25	chr5:106879800-106881800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr5:106879800-106882600	Weak transcription	HSMM	muscle
27	chr5:106879800-106883000	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr5:106879800-106884600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr5:106879800-106887800	Weak transcription	NHLF	lung
30	chr5:106879800-106888800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr5:106880000-106881600	Enhancers	Rectal Smooth Muscle	rectum
32	chr5:106880000-106885200	Weak transcription	Esophagus	oesophagus
33	chr5:106880200-106881400	Weak transcription	Colon Smooth Muscle	Colon
34	chr5:106880200-106884600	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr5:106880200-106884600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr5:106880200-106885200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr5:106880200-106889000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr5:106880400-106881400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr5:106880400-106884400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr5:106880400-106884600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr5:106880400-106885200	Weak transcription	Aorta	Aorta
42	chr5:106880400-106885400	Weak transcription	Pancreas	Pancrea
43	chr5:106880600-106882200	Enhancers	Left Ventricle	heart
44	chr5:106880600-106886800	Weak transcription	Right Ventricle	heart
45	chr5:106880800-106881400	Enhancers	Right Atrium	heart
46	chr5:106880800-106882200	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr5:106880800-106882800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr5:106880800-106884200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr5:106881000-106882000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:106881000-106882200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links