Variant report

Variant	rs3003500
Chromosome Location	chr6:53656088-53656089
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:53655984..53658850-chr6:53782726..53785660,2	MCF-7	breast:
2	chr6:53655780..53657957-chr6:53717025..53719931,2	MCF-7	breast:
3	chr6:53654376..53656765-chr6:53656869..53661036,5	MCF-7	breast:
4	chr6:53651995..53655009-chr6:53655283..53658516,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271218	Chromatin interaction
ENSG00000228614	Chromatin interaction
ENSG00000137269	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10948779	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11755346	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13220665	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2745462	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2820215	0.81[EUR][1000 genomes]
rs2820216	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3000996	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3000997	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3000999	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3001000	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3001001	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3001002	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3001009	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3001010	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3003489	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3003491	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3003493	0.89[EUR][1000 genomes]
rs3003501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34165049	0.89[EUR][1000 genomes]
rs34861916	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34880762	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35389351	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35517171	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35756855	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3813849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4236113	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4236115	0.81[AMR][1000 genomes]
rs4265033	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4276502	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4286781	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4321822	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4326237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4336450	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4351263	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4382260	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4398733	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4437471	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4484515	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4489155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4591854	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4615391	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4712048	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4712049	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4715424	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4715426	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59641455	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60035355	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6458957	0.94[EUR][1000 genomes]
rs6458958	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6458959	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6458961	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6458962	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6458965	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6458966	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6458969	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6458971	0.81[EUR][1000 genomes]
rs6650996	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6899752	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6901644	0.80[EUR][1000 genomes]
rs6920743	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6924025	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6925836	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6926478	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6937901	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71555560	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7739965	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7753504	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7754791	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7759946	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7762883	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7763081	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7763147	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7769893	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7774173	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9296719	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9296721	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9367544	0.86[EUR][1000 genomes]
rs9370235	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9370239	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9382234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9382237	0.94[EUR][1000 genomes]
rs9382250	0.80[EUR][1000 genomes]
rs9395886	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv3474747	chr6:53648744-53677210	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3474748	chr6:53648758-53677207	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53639400-53658000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:53652600-53657400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr6:53654600-53656600	Weak transcription	NHEK	skin
4	chr6:53655200-53657800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr6:53655400-53657200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:53655800-53656800	Enhancers	HepG2	liver
7	chr6:53656000-53656200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:53656000-53656200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:53656000-53657600	Enhancers	Placenta Amnion	Placenta Amnion

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