Variant report

Variant	rs731684
Chromosome Location	chr3:52109841-52109842
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52088592..52090802-chr3:52107857..52110244,2	MCF-7	breast:
2	chr3:52108818..52113062-chr3:52113432..52117079,5	K562	blood:
3	chr3:52107340..52110604-chr3:52139807..52142191,3	K562	blood:
4	chr3:52104770..52107611-chr3:52108518..52111344,2	K562	blood:
5	chr3:52101388..52103446-chr3:52108588..52110470,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164086	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12495536	0.88[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12496447	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12629791	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13316105	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2334961	1.00[CEU][hapmap];0.81[JPT][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28387060	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2878438	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs352152	0.93[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.91[EUR][1000 genomes]
rs4687607	0.94[ASW][hapmap];0.93[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4687609	0.83[MEX][hapmap]
rs4687805	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4687810	0.94[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6773704	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6777340	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6778442	0.87[ASW][hapmap];0.93[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6786592	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs735768	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs747343	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs749995	0.94[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7616695	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7644325	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs876782	0.85[LWK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs893055	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9809254	0.85[LWK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs9828327	1.00[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9843852	0.89[YRI][hapmap]
rs9846049	0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs9851576	0.94[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9866081	0.81[AMR][1000 genomes]
rs9874939	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]

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	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
3	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
4	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers 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	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
6	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
7	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

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52097400-52110800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:52097600-52119800	Weak transcription	GM12878-XiMat	blood
3	chr3:52101800-52110200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:52102000-52111200	Weak transcription	Fetal Kidney	kidney
5	chr3:52102600-52121000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:52103200-52122000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr3:52103200-52124800	Weak transcription	Colonic Mucosa	Colon
8	chr3:52103400-52114600	Weak transcription	Fetal Intestine Large	intestine
9	chr3:52105200-52110400	Weak transcription	Aorta	Aorta
10	chr3:52105200-52110400	Weak transcription	Brain Substantia Nigra	brain
11	chr3:52105600-52110400	Weak transcription	Fetal Lung	lung
12	chr3:52105600-52110800	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:52105600-52111200	Weak transcription	Osteobl	bone
14	chr3:52105600-52119600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr3:52105600-52120800	Strong transcription	Dnd41	blood
16	chr3:52105600-52124000	Weak transcription	Pancreas	Pancrea
17	chr3:52105800-52110800	Weak transcription	NHDF-Ad	bronchial
18	chr3:52105800-52112000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:52105800-52119200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:52105800-52124000	Weak transcription	Hela-S3	cervix
21	chr3:52105800-52142400	Weak transcription	Primary B cells from cord blood	blood
22	chr3:52106000-52110200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr3:52106000-52110400	Weak transcription	Brain Germinal Matrix	brain
24	chr3:52106000-52110800	Weak transcription	Right Ventricle	heart
25	chr3:52106000-52111000	Weak transcription	Fetal Heart	heart
26	chr3:52106000-52111000	Weak transcription	Lung	lung
27	chr3:52106000-52111400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:52106200-52121000	Weak transcription	HSMM	muscle
29	chr3:52106400-52110000	Strong transcription	Fetal Thymus	thymus
30	chr3:52106400-52110800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:52106400-52110800	Weak transcription	Left Ventricle	heart
32	chr3:52106400-52112000	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr3:52106400-52114400	Weak transcription	HMEC	breast
34	chr3:52106600-52111200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:52106800-52110400	Weak transcription	Brain Anterior Caudate	brain
36	chr3:52106800-52110600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr3:52106800-52111200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:52107000-52110000	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr3:52107000-52110000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:52107000-52110200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:52107000-52110400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr3:52107200-52110000	Weak transcription	Brain Cingulate Gyrus	brain
43	chr3:52107200-52123200	Weak transcription	Fetal Brain Female	brain
44	chr3:52107400-52113600	Strong transcription	Thymus	Thymus
45	chr3:52107600-52110000	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr3:52107600-52110000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:52107600-52110000	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr3:52107600-52110000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
49	chr3:52107600-52110000	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr3:52107600-52110200	Strong transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links