Variant report

Variant	rs9819885
Chromosome Location	chr3:151012896-151012897
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	chr3:151011307..151016157-chr3:151019117..151025599,7	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10513387	0.88[CEU][hapmap]
rs10513393	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13321176	1.00[CEU][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs13322120	0.82[CEU][hapmap]
rs13327359	0.81[CEU][hapmap]
rs1388625	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1549829	0.88[CEU][hapmap];1.00[LWK][hapmap]
rs1554120	0.88[CEU][hapmap]
rs17204437	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17204459	0.82[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap]
rs17282940	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17282947	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17290219	0.88[CEU][hapmap]
rs17304673	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs28386791	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28734805	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28810515	0.84[EUR][1000 genomes]
rs28831788	0.84[EUR][1000 genomes]
rs55751359	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6780660	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6792089	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73157938	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73157954	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73157974	0.93[EUR][1000 genomes]
rs73157991	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7633788	0.82[CEU][hapmap]
rs7633828	0.82[CEU][hapmap]
rs7634096	0.82[CEU][hapmap]
rs7637803	0.82[CEU][hapmap]
rs9289837	0.82[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap]
rs9812617	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9814936	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9817216	1.00[CEU][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs9821749	0.87[EUR][1000 genomes]
rs9821937	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9831242	1.00[CEU][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs9834154	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9836053	0.88[CEU][hapmap]
rs9838990	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9840232	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9841430	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9844557	0.88[CEU][hapmap]
rs9848789	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9853676	0.85[EUR][1000 genomes]
rs9854017	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs9854126	0.82[CEU][hapmap]
rs9855202	0.82[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap]
rs9856118	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9859552	0.82[CEU][hapmap]
rs9859854	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9867524	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9868643	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs9871229	0.84[EUR][1000 genomes]
rs9871624	0.88[CEU][hapmap]
rs9872645	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9875587	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9876268	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9876933	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9880395	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9881116	0.94[CEU][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.84[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	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2754555	chr3:150968302-151054302	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9819885	P2RY12	cis	normal skin	skin_eQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150984400-151022400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr3:151002400-151018000	Weak transcription	NHLF	lung
3	chr3:151002600-151044000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:151005200-151014000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:151009600-151018200	Strong transcription	HMEC	breast
6	chr3:151009800-151016000	Weak transcription	Aorta	Aorta
7	chr3:151010200-151022200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:151010400-151019000	Strong transcription	NHEK	skin
9	chr3:151010600-151018800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:151010800-151013200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:151010800-151018200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:151011200-151013400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:151011200-151018800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:151011400-151021800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:151011800-151021600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr3:151012400-151013000	Strong transcription	Esophagus	oesophagus
17	chr3:151012400-151021600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:151012600-151013200	Enhancers	Fetal Heart	heart
19	chr3:151012800-151013000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:151012800-151021600	Weak transcription	Primary neutrophils fromperipheralblood	blood

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