Variant report

Variant	rs6901563
Chromosome Location	chr6:12983504-12983505
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11757634	1.00[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11758659	0.95[ASN][1000 genomes]
rs11961007	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11963982	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13207062	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34576660	0.87[ASN][1000 genomes]
rs4236091	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4236097	0.83[ASN][1000 genomes]
rs4349811	0.81[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4380742	1.00[CEU][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4432976	0.82[CHD][hapmap]
rs4711899	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4715016	1.00[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4715023	1.00[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4715032	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4715043	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4715045	0.85[CHB][hapmap]
rs4715048	0.86[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6458568	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6899754	1.00[CEU][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6900619	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6916268	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6920970	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6924689	0.83[CHD][hapmap]
rs7341250	0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.93[ASN][1000 genomes]
rs7739717	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7743219	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7760857	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7762881	0.87[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7770277	1.00[CEU][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7774403	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7774775	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9296556	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9296580	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9369768	0.86[CHD][hapmap]
rs9369815	0.82[CHD][hapmap]
rs9381636	0.89[CHD][hapmap]
rs9463337	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9463363	0.81[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9463364	0.86[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.95[ASN][1000 genomes]
rs9473113	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9473120	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9473156	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9473188	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9473198	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9473486	0.82[CHD][hapmap]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6901563	ERVFRDE1	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12964000-12988000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr6:12974400-12986800	Weak transcription	Lung	lung
3	chr6:12976000-12990200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:12977600-12986600	Weak transcription	Aorta	Aorta
5	chr6:12978800-12987800	Weak transcription	Left Ventricle	heart
6	chr6:12979000-12986800	Weak transcription	Right Ventricle	heart
7	chr6:12979600-13001800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:12980600-12986600	Weak transcription	Brain Anterior Caudate	brain
9	chr6:12982600-12990400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:12982600-13002400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:12983400-12989000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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