Variant report

Variant	rs323887
Chromosome Location	chr3:51968429-51968430
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:51966847..51969278-chr3:52021785..52023936,2	K562	blood:
2	chr3:51965258..51969010-chr3:51974469..51977350,4	MCF-7	breast:
3	chr3:51967192..51969278-chr3:52021564..52023936,2	K562	blood:
4	chr3:51966582..51968845-chr3:52028519..52030369,2	K562	blood:
5	chr3:51967929..51972024-chr3:51972365..51975961,5	MCF-7	breast:
6	chr3:51966649..51968588-chr3:51999482..52001370,2	K562	blood:
7	chr3:51965328..51968985-chr3:51969844..51971863,5	K562	blood:

Variant related genes	Relation type
ENSG00000114767	Chromatin interaction
ENSG00000162244	Chromatin interaction
ENSG00000041880	Chromatin interaction
ENSG00000243989	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11926611	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs1566941	0.89[ASN][1000 genomes]
rs1876052	0.89[ASN][1000 genomes]
rs188953	0.93[ASW][hapmap];1.00[CEU][hapmap];0.84[LWK][hapmap];0.88[MKK][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs2015691	1.00[MEX][hapmap]
rs2271069	0.89[ASN][1000 genomes]
rs323858	1.00[MEX][hapmap]
rs323863	1.00[MEX][hapmap]
rs323864	0.80[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs323868	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs323871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[YRI][hapmap];1.00[ASN][1000 genomes]
rs323879	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323881	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323885	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs323886	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323892	1.00[MEX][hapmap]
rs323893	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.92[YRI][hapmap];1.00[ASN][1000 genomes]
rs323894	1.00[ASN][1000 genomes]
rs323895	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.92[YRI][hapmap];1.00[ASN][1000 genomes]
rs323897	1.00[MEX][hapmap]
rs323898	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755797	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3774344	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs379462	1.00[MEX][hapmap]
rs411209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4416372	0.86[CHB][hapmap]
rs4986825	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs56715917	0.89[ASN][1000 genomes]
rs61087263	0.89[ASN][1000 genomes]
rs6446166	0.85[ASN][1000 genomes]
rs7432986	1.00[MEX][hapmap]
rs7614743	0.89[ASN][1000 genomes]
rs9833784	0.82[CHB][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
3	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv590280	chr3:51967439-51978327	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51960600-51974400	Weak transcription	Fetal Brain Male	brain
2	chr3:51962600-51973200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:51963800-51974400	Weak transcription	Right Atrium	heart
4	chr3:51964000-51972800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:51964400-51972600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:51964400-51973200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:51964400-51973600	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:51964400-51973600	Strong transcription	Thymus	Thymus
9	chr3:51964600-51971400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:51964600-51972800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:51964800-51973600	Strong transcription	Skeletal Muscle Male	skeletal muscle
12	chr3:51965000-51972600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:51965000-51972800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:51965000-51972800	Strong transcription	Liver	Liver
15	chr3:51965000-51973400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:51965000-51973400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:51965000-51973400	Strong transcription	Brain Cingulate Gyrus	brain
18	chr3:51965000-51973400	Strong transcription	Brain Inferior Temporal Lobe	brain
19	chr3:51965000-51973600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:51965000-51973600	Strong transcription	Fetal Muscle Leg	muscle
21	chr3:51965000-51973600	Strong transcription	Fetal Stomach	stomach
22	chr3:51965000-51973600	Strong transcription	Lung	lung
23	chr3:51965200-51970200	Strong transcription	NH-A	brain
24	chr3:51965200-51973000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:51965200-51973600	Strong transcription	Fetal Muscle Trunk	muscle
26	chr3:51965200-51974200	Strong transcription	Primary B cells from peripheral blood	blood
27	chr3:51965200-51974600	Strong transcription	Fetal Intestine Small	intestine
28	chr3:51965400-51972800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:51965600-51971200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:51965600-51973400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:51965800-51969600	Weak transcription	Hela-S3	cervix
32	chr3:51965800-51972600	Strong transcription	Ovary	ovary
33	chr3:51965800-51973200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:51965800-51973200	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr3:51965800-51973400	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr3:51965800-51973400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:51965800-51973600	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr3:51965800-51974000	Strong transcription	NHEK	skin
39	chr3:51965800-51974400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr3:51966000-51970800	Weak transcription	NHDF-Ad	bronchial
41	chr3:51966000-51972800	Strong transcription	Pancreas	Pancrea
42	chr3:51966000-51973600	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr3:51966000-51973600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:51966000-51973600	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr3:51966000-51973600	Strong transcription	Stomach Smooth Muscle	stomach
46	chr3:51966000-51973800	Strong transcription	Osteobl	bone
47	chr3:51966000-51974000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:51966000-51974400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr3:51966200-51969200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr3:51966200-51972000	Strong transcription	GM12878-XiMat	blood

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