Variant report

Variant	rs3829094
Chromosome Location	chr9:71995487-71995488
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:71994976..71996926-chr9:72001185..72002908,2	MCF-7	breast:
2	chr9:71939667..71941572-chr9:71995013..71999921,5	MCF-7	breast:
3	chr9:71995411..71998081-chr9:71998743..72001190,2	MCF-7	breast:
4	chr9:71649254..71651788-chr9:71993811..71996699,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165060	Chromatin interaction
ENSG00000135063	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10115490	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10118562	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10746595	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[TSI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10746596	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10780321	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10780324	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10780326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10780336	0.88[ASW][hapmap];0.88[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10867426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10867436	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11138402	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11138412	0.80[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1334311	1.00[CEU][hapmap];0.84[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3892193	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4112222	0.96[CEU][hapmap];0.84[JPT][hapmap]
rs4255205	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4421413	0.84[ASW][hapmap];0.96[CEU][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.80[TSI][hapmap]
rs4458929	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4492445	0.92[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6559495	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7047788	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7870082	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv831610	chr9:71846941-72016835	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv893428	chr9:71926658-72027641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv893429	chr9:71961923-72047337	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv893430	chr9:71968730-72036369	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1047593	chr9:71971536-72180583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71979000-72001800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:71983400-72001800	Weak transcription	Brain Anterior Caudate	brain
3	chr9:71985400-72006600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr9:71986600-72002600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr9:71988800-71998600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr9:71989000-72002800	Weak transcription	Brain Substantia Nigra	brain
7	chr9:71989600-71997000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr9:71990600-72000200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr9:71991800-72012200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr9:71992000-71995800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr9:71992000-72001800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr9:71992000-72009800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr9:71992200-71997000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr9:71992200-72001800	Weak transcription	Adipose Nuclei	Adipose
15	chr9:71992400-71999400	Weak transcription	Brain Angular Gyrus	brain
16	chr9:71992400-72001800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:71992600-71996000	Weak transcription	Right Atrium	heart
18	chr9:71992600-72000800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr9:71992600-72006200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr9:71992600-72006600	Weak transcription	Esophagus	oesophagus
21	chr9:71992800-71997200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr9:71992800-71997400	Enhancers	Fetal Muscle Leg	muscle
23	chr9:71992800-71998200	Weak transcription	Ovary	ovary
24	chr9:71992800-71998400	Weak transcription	Fetal Stomach	stomach
25	chr9:71992800-72000200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr9:71992800-72001400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr9:71993000-71997000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr9:71993000-72006600	Weak transcription	Brain Hippocampus Middle	brain
29	chr9:71993600-71996000	Enhancers	HUVEC	blood vessel
30	chr9:71993600-71997200	Enhancers	Stomach Smooth Muscle	stomach
31	chr9:71993800-71996200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr9:71994000-71995800	Enhancers	Placenta	Placenta
33	chr9:71994000-71996000	Enhancers	Fetal Heart	heart
34	chr9:71994000-71997400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr9:71994000-71997400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr9:71994200-71996200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr9:71994200-71996200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr9:71994200-71996200	Enhancers	Fetal Muscle Trunk	muscle
39	chr9:71994200-71996200	Enhancers	Left Ventricle	heart
40	chr9:71994400-71995600	Weak transcription	Psoas Muscle	Psoas
41	chr9:71994400-72006800	Weak transcription	Spleen	Spleen
42	chr9:71994800-71995800	Weak transcription	Lung	lung
43	chr9:71994800-71996000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr9:71994800-71996200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr9:71994800-71996200	Enhancers	HMEC	breast
46	chr9:71994800-71996600	Enhancers	Colon Smooth Muscle	Colon
47	chr9:71994800-71998400	Weak transcription	Gastric	stomach
48	chr9:71994800-72000200	Weak transcription	Pancreas	Pancrea
49	chr9:71995000-71996000	Enhancers	Muscle Satellite Cultured Cells	--
50	chr9:71995000-71996000	Weak transcription	Placenta Amnion	Placenta Amnion

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