Variant report

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11707823	0.83[ASN][1000 genomes]
rs11711913	0.81[ASN][1000 genomes]
rs1346407	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2360021	0.95[CHB][hapmap]
rs2360026	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs3732748	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs4384925	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs495532	0.82[CHD][hapmap]
rs517729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs517738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs521694	0.91[ASN][1000 genomes]
rs527297	0.86[ASN][1000 genomes]
rs550210	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs578032	0.85[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.92[ASN][1000 genomes]
rs583190	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs587384	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs589281	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs604132	0.90[ASN][1000 genomes]
rs652424	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs661201	0.85[JPT][hapmap]
rs6809466	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs838022	0.85[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.80[LWK][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.90[ASN][1000 genomes]
rs934083	0.95[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][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	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834700	chr3:54637374-54803896	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs515920	RFT1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54705000-54719000	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr3:54705600-54718800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:54706000-54721600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr3:54706200-54719400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:54713600-54718800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:54713600-54743400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:54716000-54724800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:54717600-54725200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:54718200-54719000	Enhancers	H9 Cell Line	embryonic stem cell
10	chr3:54718400-54719200	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr3:54718600-54719000	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr3:54718600-54719000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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