Variant report

Variant	rs2726475
Chromosome Location	chr4:106249102-106249103
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11097887	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2077608	0.80[CEU][hapmap]
rs2133086	0.88[CEU][hapmap]
rs2466917	0.84[ASN][1000 genomes]
rs2466918	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2636732	0.80[CEU][hapmap]
rs2636734	0.83[CEU][hapmap]
rs2636741	0.84[CEU][hapmap]
rs2636742	0.83[CEU][hapmap]
rs2636743	0.80[CEU][hapmap]
rs2647237	0.83[ASN][1000 genomes]
rs2647238	0.91[EUR][1000 genomes]
rs2647250	0.83[CEU][hapmap]
rs2647258	0.88[ASN][1000 genomes]
rs2713831	0.80[CEU][hapmap]
rs2713834	0.80[CEU][hapmap]
rs2713860	0.84[CEU][hapmap]
rs2713863	0.84[CEU][hapmap]
rs2713873	0.80[CEU][hapmap]
rs2726455	0.80[CEU][hapmap]
rs2726479	0.88[EUR][1000 genomes]
rs2726482	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2726485	0.84[ASN][1000 genomes]
rs2726526	0.80[CEU][hapmap]
rs7670522	0.82[CEU][hapmap]
rs7678440	0.82[CEU][hapmap]
rs7683416	0.82[CEU][hapmap]
rs7698080	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs923589	0.80[CEU][hapmap]

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	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv879698	chr4:106155751-106309224	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv830027	chr4:106222010-106406738	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2726475	TET2	cis	cerebellum	SCAN
rs2726475	PPA2	cis	multi-tissue	Pritchard

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106234400-106266600	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr4:106235800-106255800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr4:106238600-106253800	Weak transcription	Left Ventricle	heart
4	chr4:106242000-106253600	Weak transcription	Aorta	Aorta
5	chr4:106245600-106266400	Weak transcription	Gastric	stomach
6	chr4:106248800-106250800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr4:106249000-106249800	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr4:106249000-106249800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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