Variant report

Variant	rs12500475
Chromosome Location	chr4:54971211-54971212
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12501838	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13114613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13142462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1364989	0.84[GIH][hapmap];0.91[MEX][hapmap]
rs34372785	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35529982	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35638196	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35818763	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41386153	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6554148	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6817230	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6842144	0.81[ASN][1000 genomes]
rs6842584	0.90[GIH][hapmap]
rs6850083	0.92[ASN][1000 genomes]
rs7695934	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	nsv879018	chr4:54714753-55030375	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1003167	chr4:54732051-55081905	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv537096	chr4:54732051-55081905	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv594202	chr4:54943432-55011123	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv594203	chr4:54960005-55030375	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54968800-54973000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr4:54969200-54973400	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr4:54970200-54971600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr4:54970600-54971600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
5	chr4:54970600-54971600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
6	chr4:54970600-54971600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:54970600-54972000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
8	chr4:54970600-54972200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
9	chr4:54970600-54975200	Weak transcription	Pancreas	Pancrea
10	chr4:54970600-54975600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:54970800-54971400	Flanking Active TSS	GM12878-XiMat	blood
12	chr4:54970800-54971600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
13	chr4:54971000-54971600	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:54971000-54972400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
15	chr4:54971200-54971400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
16	chr4:54971200-54971400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
17	chr4:54971200-54972200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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