Variant report

Variant	rs475413
Chromosome Location	chr9:97920712-97920713
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97398090..97401026-chr9:97919610..97921770,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1020962	1.00[JPT][hapmap]
rs1038092	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs10761371	1.00[JPT][hapmap]
rs10993471	1.00[JPT][hapmap]
rs12553869	1.00[JPT][hapmap]
rs12555829	1.00[JPT][hapmap]
rs1564235	1.00[JPT][hapmap]
rs1571896	1.00[JPT][hapmap]
rs1623009	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs173339	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1871220	1.00[JPT][hapmap]
rs1888944	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs2061798	1.00[JPT][hapmap]
rs2061801	1.00[JPT][hapmap]
rs2306207	1.00[JPT][hapmap]
rs242448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2655055	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2765817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs356660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs356661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs356662	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs356663	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs356671	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs356685	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs356686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3739748	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs3780560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs400727	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs420089	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4647379	1.00[MKK][hapmap]
rs4647513	1.00[MKK][hapmap];0.83[YRI][hapmap]
rs4647551	1.00[MKK][hapmap]
rs4743975	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs4743977	1.00[JPT][hapmap]
rs4743989	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4744421	1.00[JPT][hapmap]
rs4744437	0.91[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap]
rs4744440	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs607105	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs648615	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs651009	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7033294	0.83[YRI][hapmap]
rs9299427	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
2	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv831656	chr9:97831551-97989980	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97890000-97928000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr9:97893800-97940400	Weak transcription	Pancreas	Pancrea
3	chr9:97894200-97925600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:97900800-97930800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:97901600-97925000	Weak transcription	Fetal Intestine Large	intestine
6	chr9:97902000-97929800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:97905800-97924000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr9:97906400-97933000	Weak transcription	Fetal Kidney	kidney
9	chr9:97906600-97950200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr9:97910800-97933000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr9:97911200-97921000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:97911200-97930000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:97913200-97929000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr9:97913200-97930200	Weak transcription	Primary T cells from cord blood	blood
15	chr9:97913400-97929800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr9:97914200-97923400	Weak transcription	Fetal Intestine Small	intestine
17	chr9:97917400-97925200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr9:97919400-97920800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:97919400-97920800	Enhancers	GM12878-XiMat	blood
20	chr9:97919400-97920800	Enhancers	NHLF	lung
21	chr9:97919600-97920800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr9:97919600-97920800	Enhancers	Hela-S3	cervix
23	chr9:97919600-97921200	Enhancers	Muscle Satellite Cultured Cells	--
24	chr9:97919600-97921200	Enhancers	Right Ventricle	heart
25	chr9:97920000-97921200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr9:97920000-97925600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr9:97920000-97952000	Weak transcription	Aorta	Aorta
28	chr9:97920000-97952000	Weak transcription	Esophagus	oesophagus
29	chr9:97920400-97925600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr9:97920400-97930400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr9:97920400-97951800	Weak transcription	HepG2	liver
32	chr9:97920600-97923400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr9:97920600-97925200	Weak transcription	Adipose Nuclei	Adipose
34	chr9:97920600-97925200	Weak transcription	Psoas Muscle	Psoas
35	chr9:97920600-97925800	Weak transcription	Fetal Stomach	stomach
36	chr9:97920600-97930400	Weak transcription	Liver	Liver
37	chr9:97920600-97931000	Weak transcription	Fetal Lung	lung
38	chr9:97920600-97933000	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr9:97920600-97933400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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