Variant report

Variant	rs2276764
Chromosome Location	chr3:151131183-151131184
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:151097198..151097813-chr3:151130478..151131421,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10513398	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10513399	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs10935844	0.96[CEU][hapmap];0.83[CHB][hapmap];0.98[GIH][hapmap];0.95[LWK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs10935845	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs11708287	0.86[CEU][hapmap]
rs11713504	0.82[CEU][hapmap]
rs12489121	0.87[CEU][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12497065	0.81[CEU][hapmap]
rs1491974	0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs17504	0.90[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4680405	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6787801	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67886110	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9289836	0.80[YRI][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	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
2	nsv1000355	chr3:151108859-151243835	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv995048	chr3:151114074-151560019	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2276764	P2RY12	cis	Nerve Tibial	GTEx
rs2276764	P2RY12	cis	lung	GTEx
rs2276764	RHOC	trans	lymphoblastoid	seeQTL
rs2276764	P2RY12	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:151075600-151136400	Weak transcription	Fetal Brain Female	brain
2	chr3:151090200-151142400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr3:151098800-151143400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:151102200-151148600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:151102600-151132000	Weak transcription	Brain Angular Gyrus	brain
6	chr3:151102800-151136400	Weak transcription	Brain Substantia Nigra	brain
7	chr3:151102800-151150600	Weak transcription	Brain Anterior Caudate	brain
8	chr3:151104200-151139600	Weak transcription	Dnd41	blood
9	chr3:151106000-151134200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:151106000-151154600	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:151106200-151131200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:151112800-151143400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:151113200-151142600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr3:151113400-151143600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:151117600-151142600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:151119000-151142600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:151121800-151138400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:151122600-151135400	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr3:151122800-151139800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:151123200-151139600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:151124600-151139200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:151125600-151131600	Strong transcription	Primary hematopoietic stem cells	blood
23	chr3:151126800-151140200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:151126800-151148600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:151127200-151149200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr3:151128000-151132400	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr3:151129400-151137800	Weak transcription	Placenta	Placenta
28	chr3:151129400-151142400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:151129400-151162800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr3:151130800-151131400	Enhancers	Adipose Nuclei	Adipose
31	chr3:151130800-151132000	Strong transcription	Fetal Intestine Small	intestine
32	chr3:151130800-151142600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:151131000-151132400	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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