Variant report

Variant	rs1378657
Chromosome Location	chr3:160526759-160526760
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	chr3:160521593..160523754-chr3:160526329..160528531,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10513553	0.84[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12487861	0.83[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs13068380	0.94[EUR][1000 genomes]
rs1378654	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1378655	0.83[EUR][1000 genomes]
rs1378656	0.83[EUR][1000 genomes]
rs1378658	0.84[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap]
rs1455869	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes]
rs1598495	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1829716	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes]
rs1839019	0.80[JPT][hapmap]
rs1851378	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1902282	0.82[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1915929	0.89[ASN][1000 genomes]
rs2049214	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2049215	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59542611	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6775743	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6781371	0.81[EUR][1000 genomes]
rs6794047	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs718757	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs722871	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7618832	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7630250	0.89[ASN][1000 genomes]
rs7640348	0.81[EUR][1000 genomes]
rs779058	0.89[ASN][1000 genomes]
rs897494	0.83[EUR][1000 genomes]
rs972909	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9814394	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9815499	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9833075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9866566	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9868489	0.83[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9883862	0.83[EUR][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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1009249	chr3:160496237-160627378	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv536780	chr3:160496237-160627378	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 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	chr3:160520400-160529600	Weak transcription	Colonic Mucosa	Colon
2	chr3:160522800-160527600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr3:160522800-160529000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:160523000-160532800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:160523200-160528600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:160523400-160527400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:160524200-160527200	Weak transcription	Right Ventricle	heart
8	chr3:160525200-160527400	Enhancers	Brain Germinal Matrix	brain
9	chr3:160525400-160526800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:160525400-160527000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:160525800-160526800	Enhancers	Fetal Kidney	kidney
12	chr3:160525800-160528800	Enhancers	Liver	Liver
13	chr3:160525800-160529000	Enhancers	Brain Cingulate Gyrus	brain
14	chr3:160525800-160529000	Enhancers	Brain Hippocampus Middle	brain
15	chr3:160525800-160530200	Enhancers	Adipose Nuclei	Adipose
16	chr3:160525800-160530400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:160525800-160530600	Enhancers	Fetal Brain Female	brain
18	chr3:160525800-160530800	Enhancers	Fetal Brain Male	brain
19	chr3:160526000-160526800	Enhancers	Gastric	stomach
20	chr3:160526000-160527800	Enhancers	Pancreas	Pancrea
21	chr3:160526000-160528000	Enhancers	Psoas Muscle	Psoas
22	chr3:160526000-160528200	Enhancers	Right Atrium	heart
23	chr3:160526000-160528400	Enhancers	Aorta	Aorta
24	chr3:160526000-160528400	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr3:160526000-160528400	Enhancers	Left Ventricle	heart
26	chr3:160526000-160528600	Enhancers	Brain Substantia Nigra	brain
27	chr3:160526000-160528800	Enhancers	Brain Angular Gyrus	brain
28	chr3:160526000-160528800	Enhancers	Fetal Muscle Leg	muscle
29	chr3:160526000-160529200	Enhancers	Rectal Smooth Muscle	rectum
30	chr3:160526000-160530200	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr3:160526000-160530600	Enhancers	Colon Smooth Muscle	Colon
32	chr3:160526200-160526800	Enhancers	Esophagus	oesophagus
33	chr3:160526200-160526800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr3:160526200-160527400	Enhancers	Fetal Muscle Trunk	muscle
35	chr3:160526200-160528200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr3:160526200-160528600	Enhancers	Ovary	ovary
37	chr3:160526400-160526800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:160526400-160526800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr3:160526400-160526800	Enhancers	Stomach Mucosa	stomach
40	chr3:160526400-160527400	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr3:160526400-160527600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr3:160526400-160528000	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr3:160526400-160530600	Enhancers	Brain Anterior Caudate	brain
44	chr3:160526600-160527000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:160526600-160528400	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr3:160526600-160529000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:160526600-160529800	Enhancers	NHDF-Ad	bronchial
48	chr3:160526600-160530400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr3:160526600-160530400	Weak transcription	Fetal Heart	heart

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