Variant report

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10009391	0.82[JPT][hapmap]
rs10017728	0.81[JPT][hapmap]
rs10034770	0.81[JPT][hapmap]
rs10805229	0.81[JPT][hapmap]
rs11722015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13109215	0.81[JPT][hapmap]
rs13122692	0.80[JPT][hapmap]
rs13122849	0.81[JPT][hapmap]
rs13143995	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1513572	0.81[JPT][hapmap]
rs1530816	0.85[JPT][hapmap]
rs2175783	0.81[JPT][hapmap]
rs2323160	0.86[JPT][hapmap]
rs28405589	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4697241	0.81[JPT][hapmap]
rs4697244	0.86[JPT][hapmap]
rs6448098	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs6448099	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs715840	0.81[JPT][hapmap]
rs7668222	0.86[JPT][hapmap]
rs7696243	0.80[JPT][hapmap]
rs868745	0.86[JPT][hapmap]
rs966922	0.81[JPT][hapmap]
rs975792	0.99[ASN][1000 genomes]
rs987045	0.86[JPT][hapmap]

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	nsv817467	chr4:21602921-22422816	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv2757924	chr4:21873204-21980559	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv2759231	chr4:21873204-21980559	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv428440	chr4:21873204-21980559	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10938864	PPARGC1A	cis	cerebellum	SCAN
rs10938864	LCORL	cis	parietal	SCAN
rs10938864	PCNXL2	trans	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:21886200-21891600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr4:21890200-21891400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:21890400-21893200	Weak transcription	Ovary	ovary
4	chr4:21890600-21891400	Enhancers	Muscle Satellite Cultured Cells	--
5	chr4:21890600-21891600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr4:21890600-21894600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:21890600-21894800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr4:21891000-21892400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:21891200-21891600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:21891200-21899600	Weak transcription	HMEC	breast

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