Variant report

Variant	rs6458971
Chromosome Location	chr6:53743438-53743439
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10948779	0.87[EUR][1000 genomes]
rs2745461	0.86[EUR][1000 genomes]
rs2745462	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2820215	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2820216	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3000996	0.81[EUR][1000 genomes]
rs3000997	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3000999	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3001000	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3001001	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3001002	0.90[EUR][1000 genomes]
rs3001009	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3001010	0.81[EUR][1000 genomes]
rs3003489	0.91[EUR][1000 genomes]
rs3003491	0.91[EUR][1000 genomes]
rs3003493	0.91[EUR][1000 genomes]
rs3003500	0.81[EUR][1000 genomes]
rs3003501	0.81[EUR][1000 genomes]
rs3813849	0.81[EUR][1000 genomes]
rs4236113	0.91[EUR][1000 genomes]
rs4236115	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4265033	0.90[EUR][1000 genomes]
rs4276502	0.83[EUR][1000 genomes]
rs4286781	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4321822	0.82[EUR][1000 genomes]
rs4326237	0.81[EUR][1000 genomes]
rs4336450	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4351263	0.89[EUR][1000 genomes]
rs4382260	0.91[EUR][1000 genomes]
rs4398733	0.91[EUR][1000 genomes]
rs4437471	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4484515	0.91[EUR][1000 genomes]
rs4489155	0.81[EUR][1000 genomes]
rs4591854	0.91[EUR][1000 genomes]
rs4613824	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4615391	0.81[EUR][1000 genomes]
rs4712048	0.91[EUR][1000 genomes]
rs4712049	0.91[EUR][1000 genomes]
rs4715424	0.81[EUR][1000 genomes]
rs4715426	0.91[EUR][1000 genomes]
rs6458957	0.87[EUR][1000 genomes]
rs6458958	0.90[EUR][1000 genomes]
rs6458959	0.90[EUR][1000 genomes]
rs6458961	0.88[EUR][1000 genomes]
rs6458962	0.87[EUR][1000 genomes]
rs6458965	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6458966	0.91[EUR][1000 genomes]
rs6458969	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6458972	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6650996	0.90[EUR][1000 genomes]
rs6901644	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6920743	0.90[EUR][1000 genomes]
rs6924025	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6926478	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6937901	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs742524	0.89[EUR][1000 genomes]
rs7739965	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7753504	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7754791	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7762883	0.87[EUR][1000 genomes]
rs7763081	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7763147	0.90[EUR][1000 genomes]
rs7769893	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7774173	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9296719	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9296721	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9367544	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9370235	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9370239	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9382234	0.81[EUR][1000 genomes]
rs9382237	0.87[EUR][1000 genomes]
rs9382250	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9395886	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[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	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:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53709800-53762200	Weak transcription	Primary B cells from cord blood	blood
2	chr6:53719800-53747800	Weak transcription	Primary T cells from cord blood	blood
3	chr6:53722000-53748200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:53727600-53751800	Weak transcription	Thymus	Thymus
5	chr6:53729400-53748000	Weak transcription	HepG2	liver
6	chr6:53730200-53748200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:53730200-53758800	Weak transcription	Brain Anterior Caudate	brain
8	chr6:53730400-53743800	Weak transcription	Fetal Heart	heart
9	chr6:53732000-53747800	Weak transcription	HSMMtube	muscle
10	chr6:53732000-53760400	Weak transcription	Aorta	Aorta
11	chr6:53735000-53751800	Weak transcription	Gastric	stomach
12	chr6:53735400-53755600	Weak transcription	HUVEC	blood vessel
13	chr6:53736200-53751400	Weak transcription	Brain Substantia Nigra	brain
14	chr6:53737800-53744800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr6:53737800-53768400	Weak transcription	Esophagus	oesophagus
16	chr6:53738400-53747800	Weak transcription	Fetal Thymus	thymus
17	chr6:53739000-53753600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:53739000-53753600	Weak transcription	NHEK	skin
19	chr6:53739000-53767800	Weak transcription	Ovary	ovary
20	chr6:53739000-53771800	Weak transcription	Pancreas	Pancrea
21	chr6:53740000-53750600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:53740000-53752400	Weak transcription	Brain Hippocampus Middle	brain
23	chr6:53740000-53755200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr6:53740200-53747800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:53740400-53754000	Weak transcription	HSMM	muscle
26	chr6:53740400-53761000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:53741000-53743800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr6:53741800-53743800	Weak transcription	Dnd41	blood
29	chr6:53741800-53760800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:53742000-53744800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:53742200-53745200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr6:53742200-53748000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:53742200-53760800	Weak transcription	Fetal Intestine Large	intestine
34	chr6:53742200-53766200	Weak transcription	Fetal Stomach	stomach
35	chr6:53742400-53758800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:53742600-53748000	Weak transcription	Primary hematopoietic stem cells	blood
37	chr6:53742800-53744200	Weak transcription	Fetal Intestine Small	intestine
38	chr6:53743000-53743800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr6:53743000-53761800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr6:53743200-53743600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr6:53743400-53743600	Enhancers	Lung	lung
42	chr6:53743400-53744000	Enhancers	Placenta	Placenta
43	chr6:53743400-53744800	Enhancers	H1 Cell Line	embryonic stem cell

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