Variant report

Variant	rs6708079
Chromosome Location	chr2:125270232-125270233
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10445856	1.00[CHB][hapmap]
rs10445857	1.00[CHB][hapmap]
rs11123041	1.00[CEU][hapmap]
rs11123042	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs11123043	1.00[CEU][hapmap]
rs11680355	1.00[CEU][hapmap]
rs11689115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs11888989	1.00[CHB][hapmap]
rs12373656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1304052	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1394144	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes]
rs1394145	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes]
rs1503997	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes]
rs1503998	0.81[LWK][hapmap]
rs1504000	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes]
rs1504002	0.92[AFR][1000 genomes]
rs1574504	1.00[CHB][hapmap]
rs17320237	1.00[CHB][hapmap]
rs17392197	1.00[CHB][hapmap]
rs17674468	1.00[JPT][hapmap]
rs17725356	1.00[CEU][hapmap]
rs17725595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17725619	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs1827596	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes]
rs1835353	1.00[CEU][hapmap]
rs1847429	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes]
rs2003039	1.00[CHB][hapmap]
rs2089104	0.92[AFR][1000 genomes]
rs2584356	0.94[CEU][hapmap]
rs4555349	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap]
rs4848936	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap]
rs6541957	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap]
rs6541961	1.00[CHB][hapmap]
rs6707283	0.81[LWK][hapmap]
rs6711296	0.92[AFR][1000 genomes]
rs6722877	0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594672	1.00[CEU][hapmap]
rs869760	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes]
rs905630	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][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	nsv1014610	chr2:125124983-125350342	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv834355	chr2:125128585-125291043	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv834356	chr2:125141494-125315418	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv834357	chr2:125258157-125421507	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6708079	SFT2D3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:125259800-125271400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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