Variant report

Variant	rs12496550
Chromosome Location	chr3:162444231-162444232
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10936308	0.88[ASN][1000 genomes]
rs11925750	0.92[ASN][1000 genomes]
rs11926645	0.89[ASN][1000 genomes]
rs12489679	0.88[ASN][1000 genomes]
rs12496614	0.92[ASN][1000 genomes]
rs13093719	0.82[ASN][1000 genomes]
rs1353556	0.92[ASN][1000 genomes]
rs1353557	0.92[ASN][1000 genomes]
rs2361609	0.86[ASN][1000 genomes]
rs4858911	0.81[ASN][1000 genomes]
rs55807361	0.87[ASN][1000 genomes]
rs57617609	0.92[ASN][1000 genomes]
rs58194889	0.85[ASN][1000 genomes]
rs59027724	0.82[ASN][1000 genomes]
rs59307821	0.81[ASN][1000 genomes]
rs61170375	0.88[ASN][1000 genomes]
rs62294573	0.85[ASN][1000 genomes]
rs62294581	0.90[ASN][1000 genomes]
rs6441546	0.93[ASN][1000 genomes]
rs7426713	0.88[ASN][1000 genomes]
rs7652373	0.88[ASN][1000 genomes]
rs9835079	0.81[ASN][1000 genomes]
rs9839936	0.88[ASN][1000 genomes]
rs9844124	0.88[ASN][1000 genomes]
rs9867696	0.92[ASN][1000 genomes]
rs9874108	0.89[ASN][1000 genomes]
rs9883543	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006802	chr3:161921063-162599175	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv428424	chr3:162145988-163033943	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1012160	chr3:162182166-162540478	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv592201	chr3:162188625-163142162	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv470994	chr3:162217993-162945834	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1005142	chr3:162284967-162447818	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv877758	chr3:162287573-162521339	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv877759	chr3:162303276-162521339	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv877761	chr3:162346392-162521339	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv1005637	chr3:162379324-162635451	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv877762	chr3:162400620-162521339	Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv869804	chr3:162414099-162776884	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv829776	chr3:162422424-162577578	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	nsv1001282	chr3:162429561-162513137	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:162439800-162459200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr3:162441200-162447000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr3:162441800-162446400	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr3:162441800-162446600	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr3:162442200-162445200	Weak transcription	Dnd41	blood
6	chr3:162442200-162445800	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr3:162442200-162447200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:162442600-162445000	Active TSS	H9 Cell Line	embryonic stem cell
9	chr3:162442600-162445600	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr3:162443800-162444800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:162444200-162448000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr3:162444200-162453800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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