Variant report

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10804492	1.00[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs11922220	0.85[CEU][hapmap]
rs12490166	0.80[CHD][hapmap]
rs12490337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12632878	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs13074817	0.81[CHD][hapmap]
rs13079085	0.81[CHD][hapmap]
rs1355769	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs4284954	0.81[CHD][hapmap]
rs4325897	0.85[CEU][hapmap]
rs4431081	0.80[CHD][hapmap]
rs4557129	0.95[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs4682302	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs6768713	0.81[CHD][hapmap]
rs6782962	0.87[ASW][hapmap];0.90[CEU][hapmap];0.82[LWK][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs6784753	0.81[CHD][hapmap]
rs6795090	0.86[AFR][1000 genomes]
rs6801225	0.89[EUR][1000 genomes]
rs7629156	1.00[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs7630035	0.91[AFR][1000 genomes]
rs955382	0.89[EUR][1000 genomes]
rs9834030	0.81[CHD][hapmap]

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	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv829676	chr3:111464087-111619200	Genic enhancers Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6784441	GAP43	cis	parietal	SCAN
rs6784441	C3orf17	cis	parietal	SCAN
rs6784441	CD200	cis	cerebellum	SCAN
rs6784441	SAT2	trans	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111471000-111480200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:111471200-111479800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:111471200-111480000	Weak transcription	HSMM	muscle
4	chr3:111471400-111479800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr3:111471400-111480000	Weak transcription	NH-A	brain
6	chr3:111477400-111478400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:111477400-111481800	Weak transcription	Left Ventricle	heart
8	chr3:111477600-111479800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:111477600-111479800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:111477600-111480000	Enhancers	NHEK	skin
11	chr3:111477600-111484600	Enhancers	HMEC	breast
12	chr3:111477800-111479800	Enhancers	Liver	Liver
13	chr3:111478000-111480200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:111478000-111484600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:111478200-111479600	Enhancers	Pancreatic Islets	Pancreatic Islet

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