Variant report

Variant	rs9296495
Chromosome Location	chr6:12865649-12865650
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:12863028..12864927-chr6:12865342..12867413,2	MCF-7	breast:
2	chr6:12859448..12861530-chr6:12863983..12865942,2	K562	blood:
3	chr6:12863378..12865957-chr6:12874022..12876094,2	K562	blood:
4	chr6:12864394..12867910-chr6:12868654..12871064,3	MCF-7	breast:

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10434854	0.96[CHD][hapmap];0.85[ASN][1000 genomes]
rs13192344	0.88[ASN][1000 genomes]
rs13192509	0.88[ASN][1000 genomes]
rs1332840	0.88[CEU][hapmap]
rs1412740	0.88[CEU][hapmap]
rs1412742	0.88[ASN][1000 genomes]
rs1412743	0.88[ASN][1000 genomes]
rs1412751	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs1537334	0.88[ASN][1000 genomes]
rs1537335	0.88[ASN][1000 genomes]
rs1537336	0.88[ASN][1000 genomes]
rs1537337	0.88[ASN][1000 genomes]
rs1537338	0.88[ASN][1000 genomes]
rs1571996	0.85[ASN][1000 genomes]
rs1572000	0.88[CEU][hapmap]
rs1572002	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs16873431	0.88[ASN][1000 genomes]
rs16873436	0.88[ASN][1000 genomes]
rs16873447	0.88[ASN][1000 genomes]
rs16873449	0.88[ASN][1000 genomes]
rs17617207	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs2026457	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2065490	0.88[ASN][1000 genomes]
rs2065491	0.88[ASN][1000 genomes]
rs2184027	0.88[ASN][1000 genomes]
rs35278288	0.96[CHD][hapmap];0.85[ASN][1000 genomes]
rs35657920	0.96[ASN][1000 genomes]
rs3945322	0.96[CHD][hapmap];0.88[ASN][1000 genomes]
rs4142300	0.85[ASN][1000 genomes]
rs4711842	0.88[ASN][1000 genomes]
rs4711845	0.88[ASN][1000 genomes]
rs4711848	0.85[ASN][1000 genomes]
rs4714866	0.88[CEU][hapmap]
rs4714913	0.88[ASN][1000 genomes]
rs4714930	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4714931	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs5017386	0.88[ASN][1000 genomes]
rs56408440	0.85[ASN][1000 genomes]
rs57387500	0.85[ASN][1000 genomes]
rs58666803	0.85[ASN][1000 genomes]
rs60954427	0.81[ASN][1000 genomes]
rs6458461	0.92[CEU][hapmap]
rs6458493	0.88[ASN][1000 genomes]
rs6458494	0.88[ASN][1000 genomes]
rs6915402	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6915585	0.85[ASN][1000 genomes]
rs6916397	0.88[CEU][hapmap]
rs6917097	1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6924150	0.87[CEU][hapmap]
rs6938417	0.87[CEU][hapmap];0.85[TSI][hapmap]
rs6941422	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs7454135	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7757858	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs7768030	0.96[CHD][hapmap];0.85[ASN][1000 genomes]
rs7776079	0.88[CEU][hapmap];0.87[TSI][hapmap]
rs9296486	0.96[CHD][hapmap];0.88[ASN][1000 genomes]
rs9296487	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9296488	0.96[CHD][hapmap];0.88[ASN][1000 genomes]
rs9296494	0.83[TSI][hapmap]
rs9349344	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9349346	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9349350	0.96[CHD][hapmap];0.88[ASN][1000 genomes]
rs9349352	0.88[ASN][1000 genomes]
rs9357503	0.96[CHD][hapmap];0.88[ASN][1000 genomes]
rs9367239	0.88[ASN][1000 genomes]
rs9367240	0.88[ASN][1000 genomes]
rs9369605	0.88[ASN][1000 genomes]
rs9369607	0.88[ASN][1000 genomes]
rs9369612	0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9381435	0.88[ASN][1000 genomes]
rs9381436	0.88[ASN][1000 genomes]
rs9381439	0.96[CHD][hapmap];0.88[ASN][1000 genomes]
rs9381451	0.96[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9395161	0.88[ASN][1000 genomes]
rs9395162	0.88[ASN][1000 genomes]
rs9395172	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9395185	0.96[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs944766	0.88[CEU][hapmap]
rs9463106	0.88[CEU][hapmap]
rs9463110	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs9472551	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs9472672	0.82[ASN][1000 genomes]
rs9472752	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];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv830587	chr6:12769661-12939875	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv830588	chr6:12793530-12972493	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1027534	chr6:12858048-12877597	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12849800-12867000	Weak transcription	Brain Anterior Caudate	brain
2	chr6:12852000-12866000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr6:12853400-12870000	Weak transcription	Brain Germinal Matrix	brain
4	chr6:12865200-12866200	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr6:12865400-12867800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:12865600-12866200	Enhancers	H1 Cell Line	embryonic stem cell

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