Variant report

Variant	rs9834064
Chromosome Location	chr3:56590069-56590070
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF7L2	chr3:56590023-56590443	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:56589231..56591997-chr3:56715959..56718849,3	K562	blood:
2	chr3:56588153..56590621-chr3:56591371..56592977,2	K562	blood:
3	chr3:56588808..56592620-chr3:56662133..56663692,3	K562	blood:
4	chr3:56589586..56592975-chr3:56714350..56719200,6	K562	blood:
5	chr17:61042877..61045351-chr3:56589650..56591304,2	MCF-7	breast:
6	chr11:122932229..122934551-chr3:56588931..56590451,2	K562	blood:
7	chr3:56589716..56592620-chr3:56662133..56663652,2	K562	blood:

No data

Variant related genes	Relation type
CCDC66	TF binding region
ENSG00000263931	Chromatin interaction
ENSG00000180376	Chromatin interaction
ENSG00000109971	Chromatin interaction
ENSG00000163946	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10865997	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130525	0.81[MEX][hapmap]
rs12486047	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12496217	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12631156	0.81[AMR][1000 genomes]
rs1316647	0.87[YRI][hapmap]
rs13317989	0.82[ASW][hapmap];0.87[LWK][hapmap];0.81[MEX][hapmap];0.87[YRI][hapmap]
rs1388256	0.81[MEX][hapmap]
rs2291498	0.82[ASW][hapmap];0.87[LWK][hapmap];0.81[MEX][hapmap];0.87[YRI][hapmap]
rs282524	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs282525	0.81[MEX][hapmap]
rs282526	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs282530	0.81[MEX][hapmap]
rs282532	0.81[AMR][1000 genomes]
rs282533	0.83[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs282537	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs282538	0.81[AMR][1000 genomes]
rs282543	0.81[AMR][1000 genomes]
rs35349208	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3732505	0.81[MEX][hapmap]
rs3732513	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4681726	0.82[ASW][hapmap];0.87[LWK][hapmap];0.81[MEX][hapmap];0.87[YRI][hapmap]
rs4682001	0.82[ASW][hapmap];0.85[LWK][hapmap];0.81[MEX][hapmap];0.87[YRI][hapmap]
rs4974218	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4974222	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55810735	0.80[EUR][1000 genomes]
rs66873962	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6767903	0.84[YRI][hapmap]
rs6769055	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6799711	0.85[AFR][1000 genomes]
rs7612464	0.81[MEX][hapmap]
rs7639731	0.81[EUR][1000 genomes]
rs7640995	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7641898	0.91[YRI][hapmap]
rs873840	0.87[YRI][hapmap]
rs9311609	0.82[ASW][hapmap];0.87[LWK][hapmap];0.81[MEX][hapmap];0.87[YRI][hapmap]
rs953540	0.87[YRI][hapmap]
rs955248	0.96[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs9822876	0.88[ASW][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9823685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847362	0.82[ASW][hapmap];0.87[LWK][hapmap];0.81[MEX][hapmap];0.87[YRI][hapmap]
rs9867302	0.87[ASW][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.91[YRI][hapmap]
rs9872059	0.81[MEX][hapmap]
rs9873754	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9985317	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347557	chr3:56466500-56619322	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv876817	chr3:56517253-56649282	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv3417076	chr3:56590062-56591960	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9834064	C3orf63	cis	cerebellum	SCAN
rs9834064	CCDC66	Cis_1M	lymphoblastoid	RTeQTL
rs9834064	FLNB	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56590000-56590400	Enhancers	HepG2	liver
2	chr3:56590000-56592000	Active TSS	NHDF-Ad	bronchial

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