Variant report

Variant	rs12497065
Chromosome Location	chr3:151096112-151096113
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10935840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10935841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10935842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10935843	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10935845	0.82[CEU][hapmap]
rs11707416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11708287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11708767	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11709550	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11713504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11717169	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11923424	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12485508	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12488803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12489121	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12490051	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12490184	0.85[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12492266	0.92[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12493628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12497089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12498042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17204501	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17204508	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17204515	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17204536	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17283010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17283038	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17283052	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17283059	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2276764	0.81[CEU][hapmap]
rs2276765	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3732765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3821663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4679817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4680400	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680405	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4680406	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4680408	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57335550	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57781984	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59605118	0.87[EUR][1000 genomes]
rs60105866	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67886110	0.87[EUR][1000 genomes]
rs6798637	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6803771	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73159907	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73159908	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73159915	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73159920	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs765281	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs9859538	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829757	chr3:151044880-151226442	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12497065	P2RY12	cis	lung	GTEx
rs12497065	P2RY12	cis	Adipose Subcutaneous	GTEx
rs12497065	P2RY12	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:151063800-151099800	Weak transcription	Fetal Intestine Small	intestine
2	chr3:151064600-151112400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:151065600-151109400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:151065600-151115200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:151069400-151129800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:151072600-151099800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:151075400-151099800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:151075600-151136400	Weak transcription	Fetal Brain Female	brain
9	chr3:151075800-151101200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:151075800-151101400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:151079800-151105400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:151080400-151098200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:151080400-151101600	Weak transcription	Brain Anterior Caudate	brain
14	chr3:151080400-151105400	Weak transcription	Fetal Muscle Leg	muscle
15	chr3:151083000-151110400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:151084400-151098400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr3:151084400-151101600	Weak transcription	Brain Angular Gyrus	brain
18	chr3:151084400-151109200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr3:151085000-151099200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:151085400-151098400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:151086200-151102400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:151087600-151116000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:151088400-151101400	Weak transcription	Brain Substantia Nigra	brain
24	chr3:151090200-151142400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr3:151090600-151098600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr3:151091200-151100000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:151091600-151099000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:151091600-151105400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:151093800-151100400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:151095000-151099000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:151095400-151105800	Weak transcription	Fetal Thymus	thymus
32	chr3:151095400-151111000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:151095600-151096200	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr3:151095800-151102000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:151096000-151096200	Enhancers	GM12878-XiMat	blood
36	chr3:151096000-151100600	Weak transcription	Placenta	Placenta
37	chr3:151096000-151101000	Weak transcription	Left Ventricle	heart
38	chr3:151096000-151129000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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