Variant report

Variant	rs4959990
Chromosome Location	chr6:4480510-4480511
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:4479237..4481357-chr6:4482342..4483965,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1009602	0.81[ASN][1000 genomes]
rs1009603	0.88[ASN][1000 genomes]
rs1009604	0.88[ASN][1000 genomes]
rs1011087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1011088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1011089	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12525331	0.91[ASN][1000 genomes]
rs1265250	0.85[ASN][1000 genomes]
rs1265256	0.81[ASN][1000 genomes]
rs1265259	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1265260	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13195445	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571630	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2021989	0.94[ASN][1000 genomes]
rs2150231	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2181015	0.83[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap]
rs2875945	0.94[ASN][1000 genomes]
rs3929704	0.82[ASN][1000 genomes]
rs4246070	0.93[ASN][1000 genomes]
rs4959295	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959297	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959298	0.94[ASN][1000 genomes]
rs4959987	0.92[ASN][1000 genomes]
rs4959989	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959991	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959992	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4959994	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4959995	0.92[CHB][hapmap];0.81[ASN][1000 genomes]
rs4959997	0.92[CHB][hapmap]
rs4959998	1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap]
rs60221507	0.94[ASN][1000 genomes]
rs62384876	0.81[ASN][1000 genomes]
rs6914063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6930327	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7450179	0.93[ASN][1000 genomes]
rs7452972	0.93[ASN][1000 genomes]
rs7453574	0.93[ASN][1000 genomes]
rs911565	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs911566	0.93[ASN][1000 genomes]
rs911567	0.93[ASN][1000 genomes]
rs9378879	0.93[ASN][1000 genomes]
rs9378880	0.93[ASN][1000 genomes]
rs9378881	0.93[ASN][1000 genomes]
rs9378882	0.94[ASN][1000 genomes]
rs9378883	0.84[ASN][1000 genomes]
rs9392053	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9392602	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9392603	0.93[ASN][1000 genomes]
rs9405247	0.94[ASN][1000 genomes]
rs9405248	0.94[ASN][1000 genomes]
rs9405748	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9502189	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9504122	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9504123	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9504124	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462620	chr6:4255708-4481421	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv600866	chr6:4255708-4481421	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1021743	chr6:4382308-4494308	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv538111	chr6:4382308-4494308	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv3421990	chr6:4446933-4659639	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv830576	chr6:4447554-4610604	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv3366530	chr6:4471528-4865322	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4479200-4480600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:4479400-4481200	Weak transcription	Right Atrium	heart
3	chr6:4480400-4481200	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr6:4480400-4481200	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr6:4480400-4481800	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr6:4480400-4482400	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr6:4480400-4483000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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