Variant report

Variant	rs9859538
Chromosome Location	chr3:151090963-151090964
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	chr3:151063727..151066442-chr3:151089515..151092440,2	K562	blood:
2	chr3:151082763..151084486-chr3:151089231..151091784,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10935840	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10935841	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10935842	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10935843	0.89[ASN][1000 genomes]
rs11707416	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11708287	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[ASN][1000 genomes]
rs11713504	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11717169	0.85[ASN][1000 genomes]
rs11923424	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12485508	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs12488803	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12490184	0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs12492266	0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs12493628	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12497065	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12497089	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12498042	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17204501	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17204508	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17204515	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17204536	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17283010	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17283059	0.85[ASN][1000 genomes]
rs2276765	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3732765	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3821663	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4679817	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4680400	0.92[ASN][1000 genomes]
rs4680406	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4680408	0.85[ASN][1000 genomes]
rs57335550	0.85[ASN][1000 genomes]
rs57781984	0.85[ASN][1000 genomes]
rs60105866	0.85[ASN][1000 genomes]
rs6803771	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs73159907	0.85[ASN][1000 genomes]
rs73159908	0.84[ASN][1000 genomes]
rs73159915	0.87[ASN][1000 genomes]
rs73159920	0.85[ASN][1000 genomes]
rs7612010	0.82[EUR][1000 genomes]
rs9653953	1.00[CEU][hapmap];0.87[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9859538	P2RY14	cis	cerebellum	SCAN

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	chr3:151072400-151091400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:151072600-151099800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:151075400-151099800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:151075600-151136400	Weak transcription	Fetal Brain Female	brain
10	chr3:151075800-151091200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:151075800-151101200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:151075800-151101400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:151079800-151105400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr3:151080400-151098200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:151080400-151101600	Weak transcription	Brain Anterior Caudate	brain
16	chr3:151080400-151105400	Weak transcription	Fetal Muscle Leg	muscle
17	chr3:151081000-151094600	Weak transcription	Placenta	Placenta
18	chr3:151082400-151095600	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr3:151083000-151110400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:151084200-151095800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:151084400-151098400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr3:151084400-151101600	Weak transcription	Brain Angular Gyrus	brain
23	chr3:151084400-151109200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:151085000-151099200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:151085400-151098400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:151086200-151102400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:151087600-151116000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:151088400-151101400	Weak transcription	Brain Substantia Nigra	brain
29	chr3:151088600-151091200	Enhancers	NHDF-Ad	bronchial
30	chr3:151088800-151091200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:151088800-151091200	Enhancers	Osteobl	bone
32	chr3:151088800-151094400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:151090000-151091600	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:151090200-151142400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr3:151090600-151091200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:151090600-151091200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:151090600-151095400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:151090600-151098600	Weak transcription	Primary hematopoietic stem cells	blood

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