Variant report

Variant	rs1000258
Chromosome Location	chr5:116061694-116061695
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:155925817..155926573-chr5:116060845..116061700,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1027291	0.95[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1027292	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap]
rs2087871	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2087873	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2131460	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2909823	0.99[ASN][1000 genomes]
rs2909824	0.87[ASN][1000 genomes]
rs2909825	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2909826	0.87[ASN][1000 genomes]
rs2933624	0.82[ASN][1000 genomes]
rs2933627	0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs2933628	0.81[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs2933630	0.95[CHB][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2933633	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2964648	0.83[EUR][1000 genomes]
rs2964649	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2964694	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964698	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2964699	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2964701	0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap]
rs2964702	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap]
rs4512159	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7707373	0.87[ASN][1000 genomes]
rs872411	0.88[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	esv2763490	chr5:115918339-116138525	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv830456	chr5:115969066-116170718	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv527974	chr5:115987168-116303678	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv462403	chr5:115994775-116284378	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv599485	chr5:115994775-116284378	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1030056	chr5:116008971-116278725	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1033140	chr5:116035131-116314673	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:116060800-116061800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:116061400-116061800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:116061400-116062000	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr5:116061400-116068200	Enhancers	Fetal Heart	heart

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