Variant report

Variant	rs677648
Chromosome Location	chr1:216326086-216326087
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10495018	0.82[CHB][hapmap]
rs1066176	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11120739	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs11120740	0.91[CEU][hapmap];0.89[CHB][hapmap]
rs1115436	0.88[CHB][hapmap];0.88[CHD][hapmap]
rs1324330	0.87[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs17026164	0.82[CHB][hapmap]
rs17026167	0.82[CHB][hapmap]
rs17026170	0.82[CHB][hapmap]
rs17026174	0.82[CHB][hapmap]
rs17026175	0.81[CHB][hapmap]
rs17026208	0.94[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs17026219	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs1805049	0.95[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs2034960	0.91[CEU][hapmap];0.89[CHB][hapmap];0.87[EUR][1000 genomes]
rs2274117	0.87[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs2669057	0.82[CHB][hapmap]
rs301736	0.88[CHB][hapmap]
rs301737	0.88[CHB][hapmap];0.88[CHD][hapmap]
rs301742	0.88[CHB][hapmap]
rs301744	0.88[CHB][hapmap]
rs301745	0.88[CHB][hapmap];0.88[CHD][hapmap]
rs301750	0.82[CHB][hapmap]
rs301752	0.82[CHB][hapmap]
rs301759	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.98[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs301760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap]
rs3754064	0.89[CHB][hapmap];0.89[CHD][hapmap]
rs3767692	0.89[CHB][hapmap]
rs378340	0.82[CHB][hapmap]
rs401269	0.81[CHD][hapmap]
rs407590	0.81[CHB][hapmap]
rs415508	0.82[CHB][hapmap]
rs430652	1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[YRI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs439940	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs4971260	0.88[EUR][1000 genomes]
rs588516	0.82[CHB][hapmap]
rs592642	0.82[CHB][hapmap]
rs600535	0.82[CHB][hapmap]
rs62906	0.82[CHB][hapmap]
rs643416	0.86[CHB][hapmap]
rs646094	0.82[CHB][hapmap]
rs648564	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs659875	0.82[CHB][hapmap]
rs669616	0.82[CHB][hapmap]
rs696719	0.88[CHB][hapmap]
rs700015	0.89[CHB][hapmap];0.89[CHD][hapmap]
rs773498	0.91[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs9660965	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs9661602	0.94[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006504	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv535288	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv873176	chr1:216249570-216363137	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv999211	chr1:216268796-216329336	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1006028	chr1:216268796-216432545	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216318800-216326200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:216318800-216330400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:216319000-216326400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:216322800-216326200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr1:216326000-216326800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:216326000-216327000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell

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