Variant report

Variant	rs411457
Chromosome Location	chr3:52228150-52228151
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52209128..52211243-chr3:52227235..52228874,2	MCF-7	breast:
2	chr3:52087390..52089445-chr3:52228138..52231082,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs104903	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1060330	0.86[CHB][hapmap]
rs11712164	0.90[CHB][hapmap]
rs11717383	0.85[CHB][hapmap]
rs164640	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs181274	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs187084	0.95[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs34569561	0.81[CHB][hapmap]
rs34656997	0.81[ASN][1000 genomes]
rs352139	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs352140	0.81[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs352158	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs352161	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs352162	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs352163	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs352165	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs352166	0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs352167	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs352168	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs352169	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs352170	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs352171	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs353547	0.86[CHB][hapmap]
rs353551	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3852064	0.81[CHB][hapmap]
rs524986	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs610060	0.86[CHB][hapmap]
rs614288	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6445358	0.86[CHB][hapmap]
rs6802320	0.82[ASN][1000 genomes]
rs7614727	0.86[CHB][hapmap]
rs7618915	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
5	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
8	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
9	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52217600-52231600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52218800-52229800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:52220200-52230000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:52222200-52231600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr3:52223400-52228400	Weak transcription	Fetal Thymus	thymus
6	chr3:52224000-52230000	Enhancers	Ovary	ovary
7	chr3:52224600-52230800	Weak transcription	Psoas Muscle	Psoas
8	chr3:52224800-52228400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:52224800-52229400	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr3:52224800-52229400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr3:52224800-52229800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr3:52224800-52231400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:52225000-52228200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr3:52225000-52228200	Weak transcription	Fetal Intestine Small	intestine
15	chr3:52225000-52228200	Weak transcription	Small Intestine	intestine
16	chr3:52225000-52229400	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr3:52225000-52229800	Weak transcription	Left Ventricle	heart
18	chr3:52225000-52231400	Weak transcription	NH-A	brain
19	chr3:52225200-52229000	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr3:52225400-52228200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:52225400-52228400	Weak transcription	Colonic Mucosa	Colon
22	chr3:52225400-52228400	Weak transcription	Stomach Mucosa	stomach
23	chr3:52225400-52229200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr3:52225400-52229400	Weak transcription	Fetal Intestine Large	intestine
25	chr3:52225400-52231200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:52225400-52231200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:52225400-52231200	Weak transcription	Pancreas	Pancrea
28	chr3:52225400-52231200	Weak transcription	Right Atrium	heart
29	chr3:52225800-52231200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:52226000-52228200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:52226000-52228200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:52226000-52228200	Weak transcription	Fetal Stomach	stomach
33	chr3:52226000-52229200	Weak transcription	K562	blood
34	chr3:52226600-52228200	Enhancers	Stomach Smooth Muscle	stomach
35	chr3:52226600-52231600	Enhancers	Placenta	Placenta
36	chr3:52226800-52231600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:52226800-52232000	Enhancers	Spleen	Spleen
38	chr3:52227000-52230000	Enhancers	Lung	lung
39	chr3:52227200-52228200	Weak transcription	Colon Smooth Muscle	Colon
40	chr3:52227400-52228200	Enhancers	Brain Substantia Nigra	brain
41	chr3:52227400-52229400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:52227400-52229400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr3:52227400-52229600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr3:52227400-52229800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:52227400-52230800	Weak transcription	Gastric	stomach
46	chr3:52227400-52231400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:52227400-52231600	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr3:52227400-52231600	Enhancers	Fetal Muscle Trunk	muscle
49	chr3:52227600-52229200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:52227600-52229200	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links