Variant report

Variant	rs9856468
Chromosome Location	chr3:155856843-155856844
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr3:155856669-155856902	K562	blood:	n/a	chr3:155856721-155856737

Variant related genes	Relation type
KCNAB1	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10936024	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11709514	0.92[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11716256	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11718399	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13073556	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13078555	0.85[EUR][1000 genomes]
rs13093154	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs1488425	0.96[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1488426	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1488427	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1906543	0.84[EUR][1000 genomes]
rs1984473	0.96[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs3936002	0.81[MEX][hapmap]
rs4234308	0.93[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs4261831	0.96[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4359773	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4359774	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4605502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679760	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4679761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680232	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4680233	0.90[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4680234	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4680235	0.89[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4680237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56231269	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62284939	0.89[ASN][1000 genomes]
rs6441034	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs6441035	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[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]
rs6441036	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6441042	0.90[MEX][hapmap];0.84[TSI][hapmap]
rs6761966	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6778035	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs6780500	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6788449	0.85[CEU][hapmap];0.94[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6793964	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7613000	0.83[EUR][1000 genomes]
rs7617796	0.85[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7618820	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629439	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7633081	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7645641	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7652981	0.85[EUR][1000 genomes]
rs9289961	0.96[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9789968	0.85[EUR][1000 genomes]
rs9814661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9816126	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs9838322	0.94[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9842620	0.85[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9861320	0.85[CEU][hapmap];0.94[CHB][hapmap]
rs9862153	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9869649	0.94[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs9870793	0.99[ASN][1000 genomes]
rs9882088	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv592085	chr3:155827634-156012679	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9856468	SCARNA7	cis	cerebellum	SCAN
rs9856468	MLF1	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155850400-155857200	Weak transcription	Ovary	ovary
2	chr3:155850400-155861800	Weak transcription	Right Atrium	heart
3	chr3:155856800-155860600	Weak transcription	Aorta	Aorta

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