Variant report

Variant	rs9859854
Chromosome Location	chr3:151003558-151003559
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10513387	0.83[CEU][hapmap]
rs10513393	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13321176	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs13322120	0.83[CEU][hapmap]
rs13327359	0.82[CEU][hapmap]
rs1388625	0.94[CEU][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1549829	0.88[CEU][hapmap]
rs1554120	0.83[CEU][hapmap]
rs17204437	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17204459	0.82[CEU][hapmap]
rs17282940	0.94[CEU][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17282947	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17290219	0.83[CEU][hapmap]
rs17304673	0.86[CEU][hapmap];0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1920393	0.82[EUR][1000 genomes]
rs28386791	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28734805	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28810515	0.87[EUR][1000 genomes]
rs28831788	0.87[EUR][1000 genomes]
rs55751359	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6780660	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6792089	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73157938	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73157954	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73157974	0.90[EUR][1000 genomes]
rs73157991	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7633788	0.83[CEU][hapmap]
rs7633828	0.83[CEU][hapmap]
rs7634096	0.83[CEU][hapmap]
rs7637803	0.82[CEU][hapmap]
rs9289837	0.82[CEU][hapmap]
rs9812617	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9814936	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9817216	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs9819885	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9821749	0.90[EUR][1000 genomes]
rs9821937	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs9831242	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs9834154	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9836053	0.88[CEU][hapmap]
rs9838990	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9840232	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9841430	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9844557	0.88[CEU][hapmap]
rs9848789	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9853676	0.88[EUR][1000 genomes]
rs9854017	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs9855202	0.82[CEU][hapmap]
rs9856118	0.94[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9859552	0.83[CEU][hapmap]
rs9867524	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9868643	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9871229	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9871624	0.89[CEU][hapmap]
rs9872645	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9875587	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9876268	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9876933	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9880395	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9881116	0.94[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	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
rs9859854	P2RY12	cis	normal skin	skin_eQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150983000-151011000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:150984400-151022400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:150984600-151003600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:150984600-151003600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:150994600-151003600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:150999400-151011200	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr3:151002000-151010600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:151002000-151012000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:151002200-151004000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:151002200-151009600	Weak transcription	HMEC	breast
11	chr3:151002200-151010800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:151002400-151018000	Weak transcription	NHLF	lung
13	chr3:151002600-151003600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:151002600-151044000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr3:151002800-151007800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr3:151002800-151010800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:151002800-151011200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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