Variant report

Variant	rs399808
Chromosome Location	chr9:15601172-15601173
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:15551543..15553297-chr9:15600119..15601625,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164989	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10116904	1.00[ASN][1000 genomes]
rs10117524	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10118595	1.00[ASN][1000 genomes]
rs10118675	1.00[ASN][1000 genomes]
rs10119257	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119931	1.00[ASN][1000 genomes]
rs10120171	1.00[ASN][1000 genomes]
rs10121012	1.00[ASN][1000 genomes]
rs10121911	1.00[ASN][1000 genomes]
rs10121971	1.00[ASN][1000 genomes]
rs10123084	1.00[ASN][1000 genomes]
rs10124718	1.00[ASN][1000 genomes]
rs10124746	1.00[ASN][1000 genomes]
rs1041529	1.00[ASN][1000 genomes]
rs10962054	1.00[ASN][1000 genomes]
rs10962061	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12336383	1.00[ASN][1000 genomes]
rs12336445	1.00[ASN][1000 genomes]
rs12337310	1.00[ASN][1000 genomes]
rs12344963	1.00[ASN][1000 genomes]
rs12348561	1.00[ASN][1000 genomes]
rs12348564	1.00[ASN][1000 genomes]
rs12348780	1.00[ASN][1000 genomes]
rs12350062	1.00[ASN][1000 genomes]
rs12350903	1.00[ASN][1000 genomes]
rs12352398	1.00[ASN][1000 genomes]
rs12353048	1.00[ASN][1000 genomes]
rs1553727	0.93[AFR][1000 genomes]
rs175762	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202321	1.00[ASN][1000 genomes]
rs2064030	1.00[ASN][1000 genomes]
rs2202865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2665515	1.00[ASN][1000 genomes]
rs2737840	1.00[ASN][1000 genomes]
rs276434	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs276437	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs276438	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs276439	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs276440	1.00[ASN][1000 genomes]
rs276442	1.00[ASN][1000 genomes]
rs276445	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs276446	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs276450	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs276451	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2777951	1.00[ASN][1000 genomes]
rs2795125	1.00[ASN][1000 genomes]
rs2795128	1.00[ASN][1000 genomes]
rs2821525	1.00[ASN][1000 genomes]
rs2821529	1.00[ASN][1000 genomes]
rs2821542	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2821543	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2821544	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28449490	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28497163	1.00[ASN][1000 genomes]
rs28735068	0.82[EUR][1000 genomes]
rs28796681	1.00[ASN][1000 genomes]
rs28800775	1.00[ASN][1000 genomes]
rs28805077	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28808908	1.00[ASN][1000 genomes]
rs28844368	1.00[ASN][1000 genomes]
rs28882210	1.00[ASN][1000 genomes]
rs28893033	1.00[ASN][1000 genomes]
rs2891001	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3119700	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3122701	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3122705	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129711	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs365710	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs381205	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs392627	1.00[ASN][1000 genomes]
rs398117	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs398178	1.00[ASN][1000 genomes]
rs401393	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs413356	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs415157	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418153	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs424131	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs443563	0.87[EUR][1000 genomes]
rs592452	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7021840	1.00[ASN][1000 genomes]
rs7852936	1.00[ASN][1000 genomes]
rs7860339	1.00[ASN][1000 genomes]
rs796391	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs811282	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926154	1.00[ASN][1000 genomes]
rs9406518	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv892626	chr9:15389610-15694690	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv892627	chr9:15397969-15909450	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv892629	chr9:15516375-15634326	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv3407839	chr9:15530438-15665653	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv892630	chr9:15554960-15694690	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1028357	chr9:15565670-15622556	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv2752286	chr9:15578017-15794897	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv613652	chr9:15579744-15661859	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv613653	chr9:15590116-15668606	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv892631	chr9:15590116-15694690	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv892632	chr9:15590116-15869845	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15587000-15620400	Weak transcription	Pancreas	Pancrea
2	chr9:15589200-15609800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr9:15589400-15610600	Weak transcription	Thymus	Thymus
4	chr9:15592800-15614000	Weak transcription	Left Ventricle	heart
5	chr9:15599000-15601400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr9:15599000-15617800	Weak transcription	Aorta	Aorta
7	chr9:15599600-15606200	Weak transcription	Fetal Lung	lung
8	chr9:15600200-15605800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr9:15600200-15614400	Weak transcription	Gastric	stomach
10	chr9:15600600-15601200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr9:15600600-15601200	ZNF genes & repeats	Fetal Thymus	thymus
12	chr9:15600600-15617600	Weak transcription	Fetal Stomach	stomach
13	chr9:15600800-15601400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
14	chr9:15600800-15601600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
15	chr9:15601000-15601200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
16	chr9:15601000-15620000	Weak transcription	Ovary	ovary

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