Variant report

Variant	rs9872645
Chromosome Location	chr3:151034997-151034998
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr3:151034273-151035046	MCF-7	breast:	n/a	chr3:151034637-151034646 chr3:151034637-151034645 chr3:151034637-151034644 chr3:151034636-151034645
2	GATA3	chr3:151034273-151035018	MCF-7	breast:	n/a	n/a
3	SRF	chr3:151034319-151035050	HCT-116	colon:	n/a	n/a
4	SP1	chr3:151034216-151035109	HCT-116	colon:	n/a	n/a
5	FOSL2	chr3:151034323-151035017	MCF-7	breast:	n/a	chr3:151034637-151034646 chr3:151034637-151034645 chr3:151034637-151034644 chr3:151034636-151034645
6	FOSL1	chr3:151034323-151035007	HCT-116	colon:	n/a	chr3:151034637-151034646 chr3:151034637-151034645 chr3:151034637-151034644 chr3:151034636-151034645
7	GATA3	chr3:151034354-151035046	SK-N-SH	brain:	n/a	n/a
8	SP1	chr3:151034178-151035022	HCT-116	colon:	n/a	n/a

Variant related genes	Relation type
GPR87	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10513387	0.88[CEU][hapmap]
rs10513393	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13321176	1.00[CEU][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs13322120	0.82[CEU][hapmap]
rs13327359	0.81[CEU][hapmap]
rs1388625	0.94[CEU][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1549829	0.88[CEU][hapmap];1.00[LWK][hapmap]
rs1554120	0.88[CEU][hapmap]
rs17204437	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17204459	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap]
rs17282940	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17282947	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17290219	0.88[CEU][hapmap]
rs17304673	0.85[CEU][hapmap];0.90[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs28386791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28734805	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55751359	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6780660	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6792089	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs73157938	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs73157954	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73157974	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73157991	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7633788	0.82[CEU][hapmap]
rs7633828	0.82[CEU][hapmap]
rs7634096	0.82[CEU][hapmap]
rs7637803	0.82[CEU][hapmap]
rs9289837	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap]
rs9812617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9814936	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9817216	1.00[CEU][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs9819885	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]
rs9821749	0.82[EUR][1000 genomes]
rs9821937	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs9831242	1.00[CEU][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap]
rs9834154	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9836053	0.88[CEU][hapmap]
rs9838990	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9840232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9841430	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9844557	0.88[CEU][hapmap]
rs9848789	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9853676	0.80[EUR][1000 genomes]
rs9854017	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs9854126	0.82[CEU][hapmap]
rs9855202	0.82[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap]
rs9856118	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9859552	0.82[CEU][hapmap]
rs9859854	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9867524	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9868643	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9871229	0.89[AFR][1000 genomes]
rs9871624	0.88[CEU][hapmap]
rs9875587	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9876268	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9876933	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9880395	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9881116	1.00[ASW][hapmap];0.94[CEU][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap]

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
rs9872645	P2RY12	cis	normal skin	skin_eQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:151002600-151044000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:151030400-151038400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr3:151031200-151038200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr3:151032200-151035200	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr3:151032200-151039200	Enhancers	Hela-S3	cervix
6	chr3:151032800-151036000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:151032800-151036800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:151033000-151035400	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr3:151033000-151036600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:151033000-151038000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:151033400-151035000	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr3:151033400-151036400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:151034000-151037600	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr3:151034200-151035000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:151034200-151035000	Enhancers	NHLF	lung
16	chr3:151034200-151035400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:151034400-151035800	Weak transcription	A549	lung
18	chr3:151034600-151035000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:151034600-151035000	Enhancers	Osteobl	bone
20	chr3:151034600-151035200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:151034600-151035800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:151034600-151035800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:151034600-151036200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr3:151034600-151039000	Enhancers	NHDF-Ad	bronchial
25	chr3:151034800-151035000	Enhancers	Placenta	Placenta
26	chr3:151034800-151035200	Flanking Active TSS	HMEC	breast
27	chr3:151034800-151035400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:151034800-151035800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr3:151034800-151035800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr3:151034800-151036000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr3:151034800-151036000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:151034800-151036400	Enhancers	NHEK	skin
33	chr3:151034800-151036600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:151034800-151036600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:151034800-151036600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:151034800-151037200	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr3:151034800-151037800	Weak transcription	NH-A	brain
38	chr3:151034800-151038200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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