Variant report

Variant	rs9296580
Chromosome Location	chr6:12993298-12993299
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11757634	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11758659	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11961007	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11963982	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13207062	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34576660	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4236091	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4236097	0.87[ASN][1000 genomes]
rs4349811	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4380742	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4711899	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4715016	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4715023	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4715032	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4715043	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715048	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6458568	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6899754	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6900619	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6901563	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6916268	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6920970	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7341250	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7739717	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7743219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760857	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7762881	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7770277	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7774403	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7774775	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9296556	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9463337	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9463363	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9463364	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9473113	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9473120	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9473156	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473188	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9473198	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][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	esv3521000	chr6:12561306-13128519	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3521001	chr6:12561306-13128519	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv817350	chr6:12922859-13137655	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv600992	chr6:12961922-13218549	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12979600-13001800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:12982600-13002400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr6:12988800-13006000	Weak transcription	Aorta	Aorta
4	chr6:12992600-12993800	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr6:12992800-12993400	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr6:12992800-12993600	Enhancers	Left Ventricle	heart
7	chr6:12992800-12993800	Enhancers	H1 Cell Line	embryonic stem cell
8	chr6:12992800-12994000	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr6:12992800-12994000	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr6:12992800-12994200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
11	chr6:12993000-12993600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:12993000-12993800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr6:12993200-12993400	Enhancers	Right Atrium	heart
14	chr6:12993200-12993600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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