Variant report

Variant	rs4146770
Chromosome Location	chr3:151048544-151048545
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10935838	0.84[EUR][1000 genomes]
rs11922647	0.84[EUR][1000 genomes]
rs1352887	0.90[CEU][hapmap];0.86[JPT][hapmap]
rs1388622	0.86[JPT][hapmap]
rs1388623	0.86[JPT][hapmap]
rs1388626	0.89[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs1463727	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1466684	1.00[ASW][hapmap];0.90[CEU][hapmap];0.86[JPT][hapmap];0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1472121	0.95[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1491979	0.83[JPT][hapmap]
rs1491980	0.89[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs1491981	1.00[ASW][hapmap];0.90[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs1873619	0.95[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1873622	0.86[JPT][hapmap]
rs2046934	0.90[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs2172249	0.86[JPT][hapmap]
rs2242353	0.95[CEU][hapmap];0.81[GIH][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs2870517	0.86[JPT][hapmap]
rs3732764	0.86[JPT][hapmap]
rs3821667	0.90[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs3971191	0.90[CEU][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs3975401	0.84[EUR][1000 genomes]
rs3975403	0.85[JPT][hapmap]
rs3975404	0.86[JPT][hapmap]
rs4679802	0.89[CEU][hapmap];0.85[JPT][hapmap]
rs4680374	0.90[CEU][hapmap];0.86[JPT][hapmap]
rs58792455	0.81[EUR][1000 genomes]
rs6440731	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs6440732	0.90[CEU][hapmap];0.86[JPT][hapmap]
rs6440735	0.95[CEU][hapmap];0.93[GIH][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6767266	0.95[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6769397	0.89[CEU][hapmap];0.86[JPT][hapmap]
rs6782212	0.86[JPT][hapmap]
rs6790748	0.90[CEU][hapmap];0.86[JPT][hapmap]
rs6803224	0.95[CEU][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs6803841	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6809699	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs7611328	0.86[JPT][hapmap]
rs7615865	0.86[JPT][hapmap]
rs7620353	0.86[JPT][hapmap]
rs7621876	0.89[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs7622010	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7623356	0.95[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7633362	0.90[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs937124	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9820422	0.90[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs9845034	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9863821	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9863983	0.95[CEU][hapmap];0.80[GIH][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs9864095	0.95[CEU][hapmap];0.93[GIH][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs9864216	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9865758	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs9877389	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs9878459	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4146770	P2RY13	cis	parietal	SCAN
rs4146770	CLRN1	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:151045600-151056600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:151045600-151063600	Weak transcription	Brain Angular Gyrus	brain
3	chr3:151046800-151049000	Weak transcription	Right Atrium	heart
4	chr3:151047000-151055200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:151047400-151050200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr3:151047600-151049800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:151047800-151049000	Active TSS	Primary hematopoietic stem cells	blood
8	chr3:151047800-151050000	Enhancers	Adipose Nuclei	Adipose
9	chr3:151048000-151049200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr3:151048200-151049000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:151048200-151050000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:151048400-151048800	Active TSS	Primary monocytes fromperipheralblood	blood
13	chr3:151048400-151049000	Active TSS	Primary B cells from cord blood	blood
14	chr3:151048400-151051200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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