Variant report

Variant	rs6853554
Chromosome Location	chr4:106947487-106947488
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10000428	0.85[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs10003024	0.85[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs10004611	0.85[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs10008428	0.85[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10008773	1.00[ASN][1000 genomes]
rs10016884	0.85[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.86[ASN][1000 genomes]
rs10017969	0.87[ASN][1000 genomes]
rs10018910	0.86[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10027207	0.86[ASN][1000 genomes]
rs10049933	0.86[ASN][1000 genomes]
rs10084928	0.80[ASW][hapmap];0.91[CEU][hapmap];0.81[TSI][hapmap]
rs11725254	0.95[EUR][1000 genomes]
rs11732251	0.83[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs11732791	0.84[ASN][1000 genomes]
rs11931386	0.84[ASN][1000 genomes]
rs11932523	0.91[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs12513345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12639678	0.93[EUR][1000 genomes]
rs12642691	0.85[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.84[ASN][1000 genomes]
rs13101612	0.85[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs13113845	0.84[ASN][1000 genomes]
rs13114479	0.84[ASN][1000 genomes]
rs13121614	0.84[ASN][1000 genomes]
rs13138528	0.84[ASN][1000 genomes]
rs17272618	0.86[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28394440	0.96[ASN][1000 genomes]
rs28467469	0.88[ASN][1000 genomes]
rs28784652	0.85[ASN][1000 genomes]
rs28805707	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28845843	0.88[ASN][1000 genomes]
rs4307042	0.87[ASN][1000 genomes]
rs4314353	0.88[ASN][1000 genomes]
rs4355394	0.99[ASN][1000 genomes]
rs4364267	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4374692	0.84[ASN][1000 genomes]
rs4382109	0.85[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs4470632	0.96[ASN][1000 genomes]
rs4508971	0.85[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.88[ASN][1000 genomes]
rs4569824	0.84[ASN][1000 genomes]
rs4577583	0.83[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs4600995	0.85[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs6533237	1.00[ASN][1000 genomes]
rs6819081	0.90[CHD][hapmap];0.84[ASN][1000 genomes]
rs6829795	0.91[CEU][hapmap];0.81[TSI][hapmap]
rs6835216	0.91[CEU][hapmap]
rs6836198	0.85[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs6844105	0.95[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6849573	0.90[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6852388	0.88[ASN][1000 genomes]
rs7438546	0.83[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs7657975	0.91[CEU][hapmap]
rs7663321	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs7664188	0.91[CEU][hapmap]
rs7667596	0.85[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7668276	0.84[ASN][1000 genomes]
rs7669087	0.91[CEU][hapmap];0.84[TSI][hapmap]
rs7671145	0.80[ASW][hapmap];0.91[CEU][hapmap];0.84[TSI][hapmap]
rs7673101	0.85[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs7682646	0.85[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs7687657	0.89[ASN][1000 genomes]
rs7689298	0.93[ASN][1000 genomes]
rs7692652	0.85[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs7693333	0.85[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs7693448	0.84[ASN][1000 genomes]
rs9996093	0.85[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014993	chr4:106796019-106980727	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv522792	chr4:106895964-106982793	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6853554	SCYE1	Cis_1M	lymphoblastoid	RTeQTL
rs6853554	TBCK	cis	parietal	SCAN
rs6853554	MGC16169	cis	multi-tissue	Pritchard
rs6853554	TBCK	cis	lymphoblastoid	seeQTL
rs6853554	MGC16169	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106935000-106948400	Weak transcription	Aorta	Aorta

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