Variant report

Variant	rs440229
Chromosome Location	chr9:15600609-15600610
allele	C/G/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: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1039813	0.85[EUR][1000 genomes]
rs1039814	0.85[EUR][1000 genomes]
rs10481557	0.88[EUR][1000 genomes]
rs10738402	0.86[EUR][1000 genomes]
rs10756674	0.84[EUR][1000 genomes]
rs10756676	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10756677	0.85[EUR][1000 genomes]
rs10756678	0.85[EUR][1000 genomes]
rs10756679	0.81[EUR][1000 genomes]
rs10756680	0.83[EUR][1000 genomes]
rs10756686	0.82[EUR][1000 genomes]
rs10756687	0.84[EUR][1000 genomes]
rs10756688	0.83[EUR][1000 genomes]
rs10756689	0.83[EUR][1000 genomes]
rs10810399	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10810400	0.81[EUR][1000 genomes]
rs10810401	0.86[EUR][1000 genomes]
rs10810402	0.84[EUR][1000 genomes]
rs10810405	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10810407	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10810408	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10810409	0.84[EUR][1000 genomes]
rs10810410	0.86[EUR][1000 genomes]
rs10962066	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10962070	0.82[EUR][1000 genomes]
rs10962098	0.86[EUR][1000 genomes]
rs10962099	0.86[EUR][1000 genomes]
rs10962110	0.81[EUR][1000 genomes]
rs12340969	0.83[EUR][1000 genomes]
rs13291638	0.83[EUR][1000 genomes]
rs1533040	0.84[EUR][1000 genomes]
rs1812686	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2055772	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2175082	0.80[EUR][1000 genomes]
rs2457265	0.80[ASN][1000 genomes]
rs3955162	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs432452	0.81[ASN][1000 genomes]
rs4448380	0.86[EUR][1000 genomes]
rs4740615	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4740618	0.85[EUR][1000 genomes]
rs4740619	0.85[EUR][1000 genomes]
rs4740620	0.84[EUR][1000 genomes]
rs4741515	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4741517	0.85[EUR][1000 genomes]
rs4741519	0.84[EUR][1000 genomes]
rs4741520	0.80[EUR][1000 genomes]
rs4741527	0.81[EUR][1000 genomes]
rs4741528	0.83[EUR][1000 genomes]
rs4741529	0.81[EUR][1000 genomes]
rs6474931	0.84[EUR][1000 genomes]
rs6474942	0.80[EUR][1000 genomes]
rs6474945	0.81[EUR][1000 genomes]
rs7025669	0.83[EUR][1000 genomes]
rs7032877	0.80[EUR][1000 genomes]
rs7036172	0.83[EUR][1000 genomes]
rs7036674	0.83[EUR][1000 genomes]
rs7044122	0.84[EUR][1000 genomes]
rs7389023	0.86[EUR][1000 genomes]
rs7389047	0.84[EUR][1000 genomes]
rs7389629	0.87[EUR][1000 genomes]
rs7859780	0.86[EUR][1000 genomes]
rs7860623	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7863088	0.86[EUR][1000 genomes]
rs7874533	0.84[EUR][1000 genomes]
rs9696751	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9886779	0.84[EUR][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:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15587000-15620400	Weak transcription	Pancreas	Pancrea
2	chr9:15588600-15600800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr9:15588600-15601000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr9:15589200-15609800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr9:15589400-15610600	Weak transcription	Thymus	Thymus
6	chr9:15592800-15614000	Weak transcription	Left Ventricle	heart
7	chr9:15593000-15600800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr9:15599000-15601400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr9:15599000-15617800	Weak transcription	Aorta	Aorta
10	chr9:15599600-15606200	Weak transcription	Fetal Lung	lung
11	chr9:15600200-15605800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr9:15600200-15614400	Weak transcription	Gastric	stomach
13	chr9:15600600-15601200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr9:15600600-15601200	ZNF genes & repeats	Fetal Thymus	thymus
15	chr9:15600600-15617600	Weak transcription	Fetal Stomach	stomach

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