Variant report

Variant	rs13086088
Chromosome Location	chr3:143723942-143723943
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:143690187..143692443-chr3:143721634..143724583,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181744	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1025984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10513234	0.95[CEU][hapmap]
rs10513235	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11914731	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13067695	0.90[ASN][1000 genomes]
rs13068298	1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs13078840	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs13081286	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1466941	0.95[CEU][hapmap]
rs16854772	0.95[EUR][1000 genomes]
rs16854816	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16854819	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16854884	0.90[ASN][1000 genomes]
rs16854886	0.90[ASN][1000 genomes]
rs17667256	0.80[EUR][1000 genomes]
rs1867608	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1867609	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1898265	0.97[ASN][1000 genomes]
rs1961542	0.90[ASN][1000 genomes]
rs1979910	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs2011080	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2164554	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2370171	0.90[ASN][1000 genomes]
rs34372603	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34683397	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35067746	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35085196	0.99[EUR][1000 genomes]
rs35193361	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35309714	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35629416	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35649888	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35788195	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35796781	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35877644	0.95[EUR][1000 genomes]
rs35885310	0.97[ASN][1000 genomes]
rs35887108	0.90[ASN][1000 genomes]
rs35959290	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4527375	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4561830	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4611822	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4613453	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4616638	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56196484	0.80[ASN][1000 genomes]
rs59768870	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60367530	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60676654	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62268458	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62269895	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6440210	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs6440212	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6766544	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6766685	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767236	1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs6768153	0.95[CEU][hapmap]
rs6769910	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6779321	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783089	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791078	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795008	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6796460	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7610378	1.00[CEU][hapmap]
rs7611326	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7634145	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7637912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7639366	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7642551	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7642774	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7646187	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7650145	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7650172	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs920159	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9755502	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9755515	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877568	chr3:143621140-143992630	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv3365190	chr3:143642195-143925886	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv591922	chr3:143645242-143825439	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143697000-143729200	Weak transcription	Aorta	Aorta
2	chr3:143697200-143727800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr3:143699200-143737600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:143702600-143727400	Weak transcription	Pancreas	Pancrea
5	chr3:143704600-143725800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:143706400-143728000	Weak transcription	Fetal Stomach	stomach
7	chr3:143706800-143725000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:143708000-143729200	Weak transcription	Ovary	ovary
9	chr3:143708800-143729200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:143709000-143724400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:143709200-143728000	Weak transcription	NHLF	lung
12	chr3:143709200-143729000	Weak transcription	Fetal Lung	lung
13	chr3:143712000-143728600	Weak transcription	Left Ventricle	heart
14	chr3:143712200-143726600	Weak transcription	Primary T cells from cord blood	blood
15	chr3:143712800-143727400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:143713400-143726800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:143714800-143726800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:143715000-143725400	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:143715000-143726400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr3:143716600-143724000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:143717200-143726000	Weak transcription	Brain Substantia Nigra	brain
22	chr3:143717600-143729400	Weak transcription	NH-A	brain
23	chr3:143717800-143728000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr3:143719200-143724600	Weak transcription	HSMMtube	muscle
25	chr3:143721200-143727400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr3:143722600-143729400	Weak transcription	HSMM	muscle

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