Variant report

Variant	rs1716709
Chromosome Location	chr3:60657213-60657214
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs12488640	0.94[ASN][1000 genomes]
rs12632090	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs13085845	0.94[ASN][1000 genomes]
rs13086029	0.94[ASN][1000 genomes]
rs13096315	0.82[ASN][1000 genomes]
rs1620446	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1623091	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs1627302	0.83[YRI][hapmap]
rs1627398	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1716703	0.97[ASN][1000 genomes]
rs1716710	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716713	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716714	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1716717	1.00[CHB][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716718	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1716721	0.81[CHB][hapmap];1.00[GIH][hapmap]
rs1716722	0.81[CHB][hapmap];1.00[GIH][hapmap]
rs1716730	0.81[CHB][hapmap];1.00[GIH][hapmap]
rs1716732	0.95[ASN][1000 genomes]
rs1716733	0.81[ASN][1000 genomes]
rs1716734	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap]
rs1716736	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs1716739	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1716753	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs1735440	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1735443	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1735444	0.91[CHB][hapmap];0.97[GIH][hapmap];0.85[EUR][1000 genomes]
rs1735445	0.94[ASN][1000 genomes]
rs1735446	0.94[ASN][1000 genomes]
rs1735448	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1735452	0.81[ASN][1000 genomes]
rs1735454	0.81[CHB][hapmap]
rs1735457	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs1735458	0.86[ASN][1000 genomes]
rs1735463	0.86[ASN][1000 genomes]
rs1735467	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1735468	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs1735475	0.81[CHB][hapmap]
rs17627239	0.81[ASN][1000 genomes]
rs17627738	0.81[CHB][hapmap]
rs2142299	0.81[CHB][hapmap]
rs2682930	0.86[JPT][hapmap]
rs2682931	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2682945	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2682952	0.86[ASN][1000 genomes]
rs2855998	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2856056	0.81[CHB][hapmap]
rs2856058	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2856068	0.86[JPT][hapmap]
rs62249153	0.86[ASN][1000 genomes]
rs62249156	0.92[ASN][1000 genomes]
rs62249273	0.81[ASN][1000 genomes]
rs62251488	0.83[ASN][1000 genomes]
rs62251490	0.91[ASN][1000 genomes]
rs6801067	0.81[ASN][1000 genomes]
rs986687	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][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	nsv529602	chr3:60088353-60830769	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv998815	chr3:60495872-60830769	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv999828	chr3:60537384-60785274	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60653800-60660400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:60654800-60657800	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr3:60654800-60659200	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr3:60654800-60659200	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr3:60655000-60657800	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr3:60656400-60657600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:60656400-60660400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:60656400-60660400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:60656800-60657600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:60656800-60657600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:60657000-60657800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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