Variant report

Variant	rs3119699
Chromosome Location	chr9:15572744-15572745
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	chr9:15570769..15573187-chr9:15586351..15588425,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231376	Chromatin interaction

Extended variants
information (count: 172 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:164)

rs_ID	r²[population]
rs10118359	0.88[EUR][1000 genomes]
rs10119975	0.84[EUR][1000 genomes]
rs10120726	0.85[AFR][1000 genomes]
rs10121393	0.87[EUR][1000 genomes]
rs10121591	0.88[EUR][1000 genomes]
rs10122339	0.84[EUR][1000 genomes]
rs10123042	0.86[EUR][1000 genomes]
rs1039813	0.81[EUR][1000 genomes]
rs1039814	0.81[EUR][1000 genomes]
rs10481557	0.88[CEU][hapmap]
rs10733295	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs10738399	0.89[EUR][1000 genomes]
rs10756671	0.81[CEU][hapmap]
rs10756673	0.85[EUR][1000 genomes]
rs10756674	0.88[CEU][hapmap];0.92[CHB][hapmap];0.81[EUR][1000 genomes]
rs10756677	0.88[CEU][hapmap]
rs10756679	0.84[CEU][hapmap]
rs10756686	0.84[CEU][hapmap]
rs10756687	0.88[CEU][hapmap]
rs10756688	0.88[CEU][hapmap]
rs10756689	0.88[CEU][hapmap]
rs10756690	0.88[CEU][hapmap]
rs10756691	0.83[EUR][1000 genomes]
rs10756697	0.84[CEU][hapmap]
rs10810397	0.85[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs10810399	0.88[CEU][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs10810400	0.80[EUR][1000 genomes]
rs10810401	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs10810402	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10810408	0.88[CEU][hapmap]
rs10810416	0.92[CEU][hapmap];0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10810419	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs10810422	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs10810424	0.88[EUR][1000 genomes]
rs10810426	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs10810427	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs10810428	0.88[CEU][hapmap]
rs10810429	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs10810430	0.85[EUR][1000 genomes]
rs10810438	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs10810439	0.88[CEU][hapmap]
rs10810440	0.92[CEU][hapmap]
rs10962066	0.88[CEU][hapmap]
rs10962070	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs10962072	0.82[EUR][1000 genomes]
rs10962073	0.81[EUR][1000 genomes]
rs10962098	0.88[CEU][hapmap]
rs10962099	0.88[CEU][hapmap]
rs10962106	0.89[EUR][1000 genomes]
rs10962110	0.85[CEU][hapmap]
rs10962121	0.85[EUR][1000 genomes]
rs10962123	0.85[EUR][1000 genomes]
rs10962125	0.84[EUR][1000 genomes]
rs10962126	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs10962142	0.80[CEU][hapmap]
rs10962147	0.82[CEU][hapmap]
rs11792937	0.92[EUR][1000 genomes]
rs11793900	0.83[EUR][1000 genomes]
rs12004358	0.85[EUR][1000 genomes]
rs12340969	0.84[CEU][hapmap]
rs12341679	0.92[CEU][hapmap]
rs12349323	0.84[EUR][1000 genomes]
rs12352779	0.84[EUR][1000 genomes]
rs12377371	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs13301516	0.92[EUR][1000 genomes]
rs1355171	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs1396706	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs1396707	0.84[CEU][hapmap]
rs1396708	0.84[CEU][hapmap]
rs1533040	0.88[CEU][hapmap]
rs1553728	0.85[CEU][hapmap]
rs169342	0.92[CEU][hapmap];0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs183928	0.92[CEU][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1848582	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs192466	0.96[CEU][hapmap];0.87[CHB][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2055772	0.88[CEU][hapmap]
rs2175080	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs2175082	0.80[CEU][hapmap]
rs2382534	0.85[CEU][hapmap]
rs2457265	0.88[EUR][1000 genomes]
rs2457637	0.88[EUR][1000 genomes]
rs2663300	0.95[EUR][1000 genomes]
rs276432	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs276433	0.82[EUR][1000 genomes]
rs276435	0.92[CEU][hapmap];0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs276436	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs276441	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs276443	0.85[EUR][1000 genomes]
rs276444	0.99[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs276447	0.96[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs276448	0.92[CEU][hapmap];0.99[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs276449	0.92[CEU][hapmap];0.88[JPT][hapmap];0.99[AFR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs276453	0.92[CEU][hapmap];0.88[JPT][hapmap];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs276454	0.92[CEU][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs276455	0.92[CEU][hapmap];0.95[EUR][1000 genomes]
rs2821545	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28410434	0.85[EUR][1000 genomes]
rs28785887	0.80[EUR][1000 genomes]
rs3122702	0.90[EUR][1000 genomes]
rs35057009	0.85[EUR][1000 genomes]
rs36086644	0.84[EUR][1000 genomes]
rs4281189	0.92[ASN][1000 genomes]
rs432452	0.92[CEU][hapmap];0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs433849	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs442549	0.92[CEU][hapmap];0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs451878	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs4740614	0.92[CEU][hapmap];0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4740615	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs4740619	0.88[CEU][hapmap]
rs4740624	0.88[CEU][hapmap]
rs4741510	0.81[CEU][hapmap]
rs4741516	0.87[EUR][1000 genomes]
rs4741519	0.88[CEU][hapmap]
rs4741522	0.88[AFR][1000 genomes]
rs4741528	0.88[CEU][hapmap]
rs4741534	0.84[CEU][hapmap]
rs4741535	0.83[CEU][hapmap]
rs62573118	0.85[EUR][1000 genomes]
rs6474930	0.95[AFR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6474931	0.88[CEU][hapmap]
rs6474944	0.88[CEU][hapmap]
rs6474945	0.88[CEU][hapmap]
rs6474946	0.88[EUR][1000 genomes]
rs6474951	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs6474952	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs6474954	0.84[CEU][hapmap]
rs6474966	0.80[CEU][hapmap]
rs7019851	0.85[CEU][hapmap]
rs7023275	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs7024640	0.84[CEU][hapmap]
rs7025669	0.88[CEU][hapmap]
rs7030846	0.89[EUR][1000 genomes]
rs7031365	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7032755	0.80[CEU][hapmap]
rs7034484	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs7034781	0.92[CEU][hapmap]
rs7035863	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs7036172	0.88[CEU][hapmap]
rs7036285	0.84[EUR][1000 genomes]
rs7036674	0.86[CEU][hapmap]
rs7036875	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7037662	0.85[EUR][1000 genomes]
rs7037908	0.84[EUR][1000 genomes]
rs7042475	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7044122	0.82[EUR][1000 genomes]
rs7046351	0.88[EUR][1000 genomes]
rs7389629	0.88[CEU][hapmap]
rs7467156	0.89[CEU][hapmap]
rs7467207	0.92[CEU][hapmap]
rs770524	0.96[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7847144	0.84[CEU][hapmap]
rs7848511	0.88[EUR][1000 genomes]
rs7851056	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7859780	0.88[CEU][hapmap]
rs7860869	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs7863088	0.88[CEU][hapmap]
rs7866629	0.84[EUR][1000 genomes]
rs7873152	0.96[CEU][hapmap];0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7874533	0.87[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7875367	0.96[CEU][hapmap];0.97[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs9407624	0.97[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs954663	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs954664	0.83[EUR][1000 genomes]
rs9650684	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1034795	chr9:15565670-15595591	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	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

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15553800-15576200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr9:15553800-15580600	Weak transcription	Ovary	ovary
3	chr9:15553800-15592600	Weak transcription	Left Ventricle	heart
4	chr9:15554000-15590200	Weak transcription	Fetal Stomach	stomach
5	chr9:15554400-15579400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr9:15554600-15580800	Weak transcription	Brain Anterior Caudate	brain
7	chr9:15562200-15588200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr9:15562400-15583800	Weak transcription	Thymus	Thymus
9	chr9:15565000-15578800	Weak transcription	Fetal Thymus	thymus
10	chr9:15570600-15574800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr9:15571000-15574600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr9:15572200-15573200	Enhancers	Fetal Lung	lung
13	chr9:15572400-15580800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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