Variant report

Variant	rs9296721
Chromosome Location	chr6:53735269-53735270
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53657682..53662159-chr6:53731929..53736372,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228614	Chromatin interaction
ENSG00000137269	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10948779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11755346	0.83[EUR][1000 genomes]
rs13220665	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2745462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820216	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3000996	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3000997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3000999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001000	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001001	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001002	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3001009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001010	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3003489	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3003491	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3003493	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs3003500	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3003501	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34861916	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34880762	0.83[EUR][1000 genomes]
rs35389351	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35517171	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs35756855	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3813849	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4236113	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4236115	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4265033	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4276502	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4286781	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4321822	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4326237	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4336450	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4351263	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4382260	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4398733	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4437471	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4484515	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4489155	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4591854	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4613824	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4615391	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4712048	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4712049	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4715424	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4715426	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59641455	0.83[EUR][1000 genomes]
rs60035355	0.83[EUR][1000 genomes]
rs6458957	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6458958	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6458959	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6458961	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6458962	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6458965	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458966	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6458969	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458971	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6458972	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6650996	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6899752	0.83[EUR][1000 genomes]
rs6901644	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6920743	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6924025	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925836	0.83[EUR][1000 genomes]
rs6926478	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6937901	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71555560	0.83[EUR][1000 genomes]
rs742524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs7739965	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7753504	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7754791	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7759946	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs7762883	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7763081	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7763147	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7769893	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7774173	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296719	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9367544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370235	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382234	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9382237	0.94[EUR][1000 genomes]
rs9382250	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9395886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9474694	1.00[CHB][hapmap]

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	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	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53695000-53743200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:53709800-53762200	Weak transcription	Primary B cells from cord blood	blood
3	chr6:53719800-53747800	Weak transcription	Primary T cells from cord blood	blood
4	chr6:53720600-53741400	Weak transcription	Dnd41	blood
5	chr6:53720800-53736600	Weak transcription	Fetal Thymus	thymus
6	chr6:53722000-53748200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:53723400-53736800	Weak transcription	Stomach Mucosa	stomach
8	chr6:53727600-53751800	Weak transcription	Thymus	Thymus
9	chr6:53728600-53738600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:53728600-53738600	Weak transcription	NHEK	skin
11	chr6:53729400-53736600	Weak transcription	Fetal Intestine Small	intestine
12	chr6:53729400-53738800	Weak transcription	Pancreas	Pancrea
13	chr6:53729400-53748000	Weak transcription	HepG2	liver
14	chr6:53730200-53748200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr6:53730200-53758800	Weak transcription	Brain Anterior Caudate	brain
16	chr6:53730400-53737200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr6:53730400-53743800	Weak transcription	Fetal Heart	heart
18	chr6:53732000-53739400	Weak transcription	Brain Hippocampus Middle	brain
19	chr6:53732000-53747800	Weak transcription	HSMMtube	muscle
20	chr6:53732000-53760400	Weak transcription	Aorta	Aorta
21	chr6:53734200-53735400	Enhancers	HUVEC	blood vessel
22	chr6:53734600-53741400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:53734800-53736200	Enhancers	Brain Substantia Nigra	brain
24	chr6:53735000-53739400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:53735000-53751800	Weak transcription	Gastric	stomach
26	chr6:53735200-53738600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:53735200-53738600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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