Variant report

Variant	rs1553081
Chromosome Location	chr3:159506128-159506129
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:159480418..159485166-chr3:159503972..159508876,8	MCF-7	breast:
2	chr3:159504199..159507462-chr3:159515627..159518397,3	MCF-7	breast:
3	chr3:159490266..159491970-chr3:159504872..159507711,2	MCF-7	breast:
4	chr3:159504230..159507022-chr3:159529536..159532354,2	MCF-7	breast:
5	chr3:159504063..159506884-chr3:159510912..159512830,2	K562	blood:
6	chr3:159505829..159507763-chr3:159508214..159510388,2	K562	blood:
7	chr3:159504853..159507555-chr3:159550828..159552388,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250588	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1009058	0.90[CEU][hapmap]
rs10936179	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1107061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11715088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12490735	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12491535	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1497762	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1675496	0.89[CEU][hapmap]
rs2010748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2169305	0.91[CHB][hapmap];0.90[ASN][1000 genomes]
rs3851359	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3889309	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3889310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4679863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4679865	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680521	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680524	1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs56107912	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62270387	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62270397	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6763138	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6771478	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6780187	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7639937	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9878736	0.86[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv4084	chr3:159492488-159513251	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159493600-159509200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr3:159493600-159516200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:159499800-159506400	Enhancers	Brain Inferior Temporal Lobe	brain
4	chr3:159500400-159509200	Enhancers	HepG2	liver
5	chr3:159501000-159508000	Enhancers	Colon Smooth Muscle	Colon
6	chr3:159501200-159506200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:159501800-159507600	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr3:159501800-159510200	Enhancers	Fetal Intestine Large	intestine
9	chr3:159502000-159522800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:159502200-159509000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:159502400-159506800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:159502400-159508000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:159502400-159508600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:159502600-159506400	Enhancers	Osteobl	bone
15	chr3:159502800-159506800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:159502800-159508000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:159503000-159506200	Enhancers	NHDF-Ad	bronchial
18	chr3:159503000-159506400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:159503000-159506400	Enhancers	NHLF	lung
20	chr3:159503000-159510200	Enhancers	Fetal Intestine Small	intestine
21	chr3:159503200-159506200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:159503400-159508000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:159503600-159506400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:159503600-159508000	Enhancers	Duodenum Mucosa	Duodenum
25	chr3:159503800-159509600	Enhancers	Adipose Nuclei	Adipose
26	chr3:159504000-159518600	Enhancers	Brain Hippocampus Middle	brain
27	chr3:159504200-159518400	Enhancers	Brain Substantia Nigra	brain
28	chr3:159504400-159506200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:159504400-159506400	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr3:159504400-159506400	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr3:159504400-159506400	Enhancers	Esophagus	oesophagus
32	chr3:159504400-159506400	Enhancers	Left Ventricle	heart
33	chr3:159504400-159506400	Enhancers	Right Atrium	heart
34	chr3:159504400-159506600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:159504400-159506600	Enhancers	Fetal Heart	heart
36	chr3:159504400-159506600	Enhancers	Placenta	Placenta
37	chr3:159504400-159507400	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr3:159504400-159508000	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr3:159504400-159508200	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr3:159504400-159508200	Enhancers	Brain Cingulate Gyrus	brain
41	chr3:159504400-159509000	Enhancers	Liver	Liver
42	chr3:159504600-159506400	Enhancers	Stomach Mucosa	stomach
43	chr3:159504600-159509400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:159504600-159511200	Enhancers	Brain Anterior Caudate	brain
45	chr3:159504800-159506400	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr3:159504800-159506600	Enhancers	Fetal Lung	lung
47	chr3:159504800-159508800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:159505000-159506200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
49	chr3:159505000-159506200	Flanking Active TSS	NH-A	brain
50	chr3:159505000-159507200	Enhancers	Small Intestine	intestine

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