Variant report

Variant	rs12654572
Chromosome Location	chr5:28396041-28396042
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10035364	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10077425	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10472610	0.89[EUR][1000 genomes]
rs10472611	0.80[EUR][1000 genomes]
rs10472612	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12652450	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12652480	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12652497	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13167301	0.83[EUR][1000 genomes]
rs4260681	0.83[AMR][1000 genomes]
rs4282327	0.84[AMR][1000 genomes]
rs4302599	0.89[EUR][1000 genomes]
rs4302600	0.83[EUR][1000 genomes]
rs4330470	0.85[AMR][1000 genomes]
rs4340932	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4443428	0.85[AMR][1000 genomes]
rs4507496	0.84[AMR][1000 genomes]
rs5001523	0.83[EUR][1000 genomes]
rs6867663	0.89[EUR][1000 genomes]
rs6872920	0.88[EUR][1000 genomes]
rs6889111	0.83[EUR][1000 genomes]
rs7710853	0.83[ASN][1000 genomes]
rs7716855	0.83[ASN][1000 genomes]
rs7724139	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7724621	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7728791	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7728805	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7729724	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9292253	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9632400	0.89[EUR][1000 genomes]
rs9632401	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880550	chr5:27863157-28732126	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1026700	chr5:28067287-28978638	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv537707	chr5:28067287-28978638	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1017761	chr5:28270595-28494470	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv537709	chr5:28270595-28494470	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1029219	chr5:28370908-29086506	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv537710	chr5:28370908-29086506	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:28391800-28397600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr5:28391800-28397600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:28391800-28397800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr5:28391800-28404000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr5:28392000-28397400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr5:28394400-28397600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr5:28394600-28397200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr5:28395600-28397800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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