Variant report

Variant	rs12485508
Chromosome Location	chr3:151101746-151101747
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10935840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935841	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935842	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10935843	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11707416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11708287	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11708767	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11709550	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11713504	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717169	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11923424	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12488803	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12489121	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs12490051	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12490184	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12492266	0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12493628	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12497065	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]
rs12497089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12498042	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17204501	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17204508	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17204515	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17204536	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17283010	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17283038	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs17283052	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17283059	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2276765	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3732765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3821663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4679817	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4680400	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680405	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4680406	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4680408	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57335550	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57781984	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59605118	0.88[EUR][1000 genomes]
rs60105866	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67886110	0.87[EUR][1000 genomes]
rs6798637	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6803771	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73159907	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73159908	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73159915	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73159920	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs765281	1.00[CEU][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes]
rs9859538	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.91[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
rs12485508	P2RY12	cis	Artery Tibial	GTEx
rs12485508	P2RY12	cis	Adipose Subcutaneous	GTEx
rs12485508	P2RY12	cis	lung	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:151064600-151112400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:151065600-151109400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:151065600-151115200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:151069400-151129800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:151075600-151136400	Weak transcription	Fetal Brain Female	brain
6	chr3:151079800-151105400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:151080400-151105400	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:151083000-151110400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:151084400-151109200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:151086200-151102400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:151087600-151116000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:151090200-151142400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr3:151091600-151105400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:151095400-151105800	Weak transcription	Fetal Thymus	thymus
15	chr3:151095400-151111000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:151095800-151102000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:151096000-151129000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:151096600-151112400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:151097800-151107800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr3:151097800-151108800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:151098800-151143400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:151099000-151103600	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:151099200-151102800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:151099400-151105400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:151099400-151107600	Enhancers	Primary B cells from peripheral blood	blood
26	chr3:151099400-151109000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr3:151099600-151107600	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr3:151099800-151101800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:151099800-151101800	Enhancers	Fetal Intestine Small	intestine
30	chr3:151099800-151103000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:151099800-151103400	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr3:151099800-151107800	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr3:151100000-151102000	Enhancers	Primary hematopoietic stem cells	blood
34	chr3:151100000-151102600	Enhancers	Fetal Intestine Large	intestine
35	chr3:151100200-151103000	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr3:151100600-151102000	Strong transcription	Placenta	Placenta
37	chr3:151100600-151102000	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr3:151100600-151102200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr3:151100600-151104000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr3:151100800-151101800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:151100800-151102600	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr3:151100800-151102800	Active TSS	Brain Hippocampus Middle	brain
43	chr3:151101000-151101800	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr3:151101000-151102600	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr3:151101000-151102600	Enhancers	Small Intestine	intestine
46	chr3:151101000-151104800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr3:151101200-151102200	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr3:151101200-151102800	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr3:151101200-151102800	Active TSS	Right Atrium	heart
50	chr3:151101400-151101800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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