Variant report

Variant	rs17429379
Chromosome Location	chr2:98967537-98967538
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98966148..98968083-chr2:98968184..98969887,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VWA3B-1	chr2:98967247-98967603	ENSG00000227987.1

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1010387	0.83[CEU][hapmap]
rs11684899	0.81[EUR][1000 genomes]
rs11691306	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs13430738	0.83[CEU][hapmap]
rs17427608	0.81[EUR][1000 genomes]
rs17427825	0.81[EUR][1000 genomes]
rs17428745	0.97[EUR][1000 genomes]
rs17428990	0.97[EUR][1000 genomes]
rs17500406	0.82[EUR][1000 genomes]
rs17501094	0.97[EUR][1000 genomes]
rs4564827	0.83[CEU][hapmap]
rs62155312	0.95[EUR][1000 genomes]
rs62155317	0.94[EUR][1000 genomes]
rs62155347	0.94[EUR][1000 genomes]
rs62155354	0.95[EUR][1000 genomes]
rs62155355	0.96[EUR][1000 genomes]
rs62155358	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62156265	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62156266	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62156268	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62156269	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62156305	0.82[EUR][1000 genomes]
rs62156724	0.81[EUR][1000 genomes]
rs62156744	0.81[EUR][1000 genomes]
rs62157892	0.81[EUR][1000 genomes]
rs62157901	0.80[EUR][1000 genomes]
rs62157907	0.81[EUR][1000 genomes]
rs62157908	0.81[EUR][1000 genomes]
rs62157916	0.82[EUR][1000 genomes]
rs72817785	0.81[EUR][1000 genomes]
rs72817792	0.81[EUR][1000 genomes]
rs72817793	0.81[EUR][1000 genomes]
rs72819903	0.93[EUR][1000 genomes]
rs72819917	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72819919	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72819921	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72819925	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72819927	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1004082	chr2:98792256-98967681	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv535833	chr2:98792256-98967681	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1008645	chr2:98915767-99010743	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1010466	chr2:98938886-98998109	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1013617	chr2:98943377-99004173	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98964800-98970000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:98965800-98972400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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