Variant report

Variant	rs9296719
Chromosome Location	chr6:53702049-53702050
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10948779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11755346	0.85[EUR][1000 genomes]
rs13220665	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs2745462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820216	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3000996	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3000997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3000999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001000	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001001	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001002	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3001009	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]
rs3001010	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3003489	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3003491	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3003493	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3003500	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3003501	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34861916	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34880762	0.85[EUR][1000 genomes]
rs35389351	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35517171	0.85[EUR][1000 genomes]
rs35756855	0.83[EUR][1000 genomes]
rs3813849	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4236113	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4236115	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4265033	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4276502	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4286781	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4321822	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4326237	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4336450	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4351263	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4382260	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4398733	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4437471	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4484515	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4489155	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4591854	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4615391	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4712048	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4712049	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4715424	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4715426	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59641455	0.85[EUR][1000 genomes]
rs60035355	0.85[EUR][1000 genomes]
rs6458957	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6458958	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6458959	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6458961	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6458962	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6458965	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458966	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6458969	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458971	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6458972	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6650996	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6899752	0.85[EUR][1000 genomes]
rs6901644	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6920743	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6924025	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925836	0.85[EUR][1000 genomes]
rs6926478	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6937901	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71555560	0.85[EUR][1000 genomes]
rs742524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7739965	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7753504	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7754791	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7759946	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs7762883	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7763081	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7763147	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7769893	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7774173	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370235	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382234	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9382237	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9382250	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9395886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[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:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53680400-53721600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:53684000-53710200	Weak transcription	Primary T cells from cord blood	blood
3	chr6:53692600-53702600	Weak transcription	Aorta	Aorta
4	chr6:53693400-53720000	Weak transcription	Left Ventricle	heart
5	chr6:53694000-53708400	Weak transcription	Fetal Thymus	thymus
6	chr6:53695000-53702600	Weak transcription	Gastric	stomach
7	chr6:53695000-53705600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:53695000-53710000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr6:53695000-53719800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:53695000-53743200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:53696200-53702600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr6:53696400-53708400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr6:53696600-53702600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr6:53697200-53718600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr6:53698000-53702200	Weak transcription	Colon Smooth Muscle	Colon
16	chr6:53698000-53702600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:53698000-53715600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr6:53698200-53702200	Weak transcription	Thymus	Thymus
19	chr6:53698200-53702600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr6:53698200-53702800	Weak transcription	HSMMtube	muscle
21	chr6:53698200-53702800	Weak transcription	HUVEC	blood vessel
22	chr6:53698400-53702600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:53698600-53702600	Weak transcription	HMEC	breast
24	chr6:53699000-53704800	Weak transcription	Fetal Intestine Small	intestine
25	chr6:53699200-53702600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr6:53699200-53703400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr6:53699400-53702200	Weak transcription	Brain Anterior Caudate	brain
28	chr6:53699400-53702400	Weak transcription	Fetal Heart	heart
29	chr6:53699400-53702600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:53699400-53702600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:53699400-53709200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr6:53700000-53704800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr6:53700200-53703000	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr6:53700400-53709200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:53700800-53702400	Enhancers	Brain Germinal Matrix	brain
36	chr6:53701000-53702800	Weak transcription	HepG2	liver
37	chr6:53701200-53702200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr6:53701200-53702600	Weak transcription	Pancreas	Pancrea
39	chr6:53701400-53702600	Enhancers	Rectal Smooth Muscle	rectum
40	chr6:53701600-53702800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:53701800-53702400	Enhancers	Brain Hippocampus Middle	brain
42	chr6:53701800-53702600	Enhancers	Brain Angular Gyrus	brain
43	chr6:53701800-53702600	Weak transcription	Brain Substantia Nigra	brain
44	chr6:53702000-53702600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:53702000-53702600	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr6:53702000-53702800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr6:53702000-53702800	Enhancers	Brain Cingulate Gyrus	brain
48	chr6:53702000-53703200	Enhancers	NHEK	skin
49	chr6:53702000-53704600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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