Variant report

Variant	rs9844680
Chromosome Location	chr3:110337794-110337795
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:110337784..110340050-chr3:110340181..110342150,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10470379	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28568711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28734003	1.00[AMR][1000 genomes]
rs4234396	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4234397	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4234399	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4317132	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4408891	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4461448	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4493460	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4507291	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4515084	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4521263	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4605580	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4635740	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4682015	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4682016	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57330466	1.00[AMR][1000 genomes]
rs57708443	1.00[AMR][1000 genomes]
rs59933690	1.00[AMR][1000 genomes]
rs60260569	1.00[AMR][1000 genomes]
rs60278991	1.00[AMR][1000 genomes]
rs60455967	1.00[AMR][1000 genomes]
rs6762712	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7614893	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7637213	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9816637	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9818929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9822353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9827059	1.00[AMR][1000 genomes]
rs9836317	1.00[AMR][1000 genomes]
rs9838031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9838218	1.00[AMR][1000 genomes]
rs9838405	1.00[AMR][1000 genomes]
rs9843913	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9855005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9857475	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9876520	1.00[AMR][1000 genomes]
rs9880132	1.00[AMR][1000 genomes]
rs9882383	1.00[AMR][1000 genomes]
rs9883414	1.00[AMR][1000 genomes]
rs9883442	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999414	chr3:110103126-110340180	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv520365	chr3:110155172-110441165	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1001144	chr3:110158316-110431113	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv536687	chr3:110158316-110431113	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1001810	chr3:110158316-110522247	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1010230	chr3:110204439-110588814	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv536688	chr3:110204439-110588814	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv829672	chr3:110206693-110361632	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1011034	chr3:110209344-110559021	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv536689	chr3:110209344-110559021	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1003106	chr3:110264476-111105943	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv1014199	chr3:110293896-110754155	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv1012854	chr3:110333519-110356714	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:110336800-110338200	Enhancers	Liver	Liver
2	chr3:110337400-110338000	Enhancers	Stomach Mucosa	stomach
3	chr3:110337600-110338200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:110337600-110338200	Enhancers	Fetal Heart	heart
5	chr3:110337600-110338600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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