Variant report

Variant	rs17427825
Chromosome Location	chr2:98893761-98893762
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1010387	0.83[CEU][hapmap];1.00[AFR][1000 genomes]
rs11684812	1.00[AFR][1000 genomes]
rs11684899	1.00[AFR][1000 genomes]
rs11691306	0.82[CEU][hapmap];1.00[AFR][1000 genomes]
rs13402201	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13430738	0.83[CEU][hapmap]
rs17427608	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17428745	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17428990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17429379	0.81[EUR][1000 genomes]
rs17500406	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17501094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4564827	0.83[CEU][hapmap]
rs62155312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62155317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62155347	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62155354	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62155355	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62155358	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62156265	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62156266	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62156268	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62156269	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62156346	1.00[AFR][1000 genomes]
rs62156681	0.90[AMR][1000 genomes]
rs62156686	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62156724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62156744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62157892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62157901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62157907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62157908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62157916	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72817785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72817792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72817793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72819903	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72819917	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72819919	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72819921	0.81[EUR][1000 genomes]
rs72819925	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72819927	0.86[AMR][1000 genomes];0.81[EUR][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	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	nsv1002366	chr2:98877050-98904494	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	1 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	chr2:98888800-98897000	Weak transcription	Ovary	ovary
2	chr2:98891000-98894200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:98892600-98893800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:98893000-98894200	Enhancers	Brain Germinal Matrix	brain
5	chr2:98893400-98894200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:98893400-98894200	Enhancers	Fetal Muscle Leg	muscle
7	chr2:98893600-98894200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:98893600-98894200	Enhancers	Fetal Muscle Trunk	muscle
9	chr2:98893600-98894400	Enhancers	Fetal Kidney	kidney
10	chr2:98893600-98895600	Enhancers	Placenta	Placenta
11	chr2:98893600-98897000	Enhancers	Rectal Mucosa Donor 31	rectum

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