Variant report

Variant	rs9830293
Chromosome Location	chr3:52147485-52147486
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52140403..52143176-chr3:52145230..52148198,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs123681	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12386365	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13314125	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13319566	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs164638	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs164639	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17051957	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17051977	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171294	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs183029	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304505	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28452586	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28659792	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352146	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs352147	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352148	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352149	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352150	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352151	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352153	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55664415	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55834589	0.88[EUR][1000 genomes]
rs56281986	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56322622	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57335685	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57466127	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59890038	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781635	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72964042	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72964044	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7638246	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808787	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs876782	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs893056	0.94[EUR][1000 genomes]
rs9809254	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9809977	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811707	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9815010	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9816434	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9817653	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9841469	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843299	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843852	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846049	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9847073	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847092	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857878	0.94[EUR][1000 genomes]
rs9860982	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9868101	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882775	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	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
4	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
5	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

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52110600-52179400	Weak transcription	Brain Germinal Matrix	brain
2	chr3:52124200-52157200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:52126200-52160600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:52128600-52157000	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr3:52129200-52155400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:52132200-52155200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:52133200-52162000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:52133400-52155000	Weak transcription	Osteobl	bone
9	chr3:52136600-52153600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:52136800-52154400	Weak transcription	Hela-S3	cervix
11	chr3:52136800-52155000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:52136800-52156000	Weak transcription	A549	lung
13	chr3:52136800-52187200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:52137200-52152400	Weak transcription	GM12878-XiMat	blood
15	chr3:52138200-52153800	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr3:52138800-52149400	Strong transcription	Thymus	Thymus
17	chr3:52139600-52151400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:52139600-52154600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr3:52139800-52153800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:52140400-52178200	Strong transcription	Dnd41	blood
21	chr3:52140600-52160800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:52140800-52155000	Weak transcription	Primary T cells from cord blood	blood
23	chr3:52141400-52151400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:52141400-52154800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:52142200-52148600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:52142400-52148600	Weak transcription	HMEC	breast
27	chr3:52142600-52148000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:52142800-52148800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:52143000-52151800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:52143000-52153800	Weak transcription	K562	blood
31	chr3:52143000-52154000	Weak transcription	NHLF	lung
32	chr3:52143000-52155000	Weak transcription	NH-A	brain
33	chr3:52143000-52156000	Weak transcription	Liver	Liver
34	chr3:52143200-52148000	Weak transcription	Esophagus	oesophagus
35	chr3:52143200-52151400	Weak transcription	Brain Substantia Nigra	brain
36	chr3:52143200-52153200	Weak transcription	Placenta	Placenta
37	chr3:52143200-52154600	Weak transcription	NHDF-Ad	bronchial
38	chr3:52143200-52156000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:52143400-52155400	Weak transcription	HSMM	muscle
40	chr3:52144200-52152800	Weak transcription	Spleen	Spleen
41	chr3:52144200-52154600	Strong transcription	Fetal Stomach	stomach
42	chr3:52144200-52155000	Weak transcription	Stomach Mucosa	stomach
43	chr3:52144200-52155200	Weak transcription	HUVEC	blood vessel
44	chr3:52144200-52163600	Weak transcription	Aorta	Aorta
45	chr3:52144400-52149000	Strong transcription	Fetal Thymus	thymus
46	chr3:52144400-52150400	Weak transcription	Brain Angular Gyrus	brain
47	chr3:52144400-52154400	Weak transcription	Fetal Intestine Large	intestine
48	chr3:52144600-52150400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr3:52144800-52148600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:52144800-52149000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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