Variant report

Variant	rs6926478
Chromosome Location	chr6:53704695-53704696
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	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11755346	0.85[EUR][1000 genomes]
rs13220665	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs2745462	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820215	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820216	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3000996	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3000997	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3000999	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001000	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001001	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001002	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3001009	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001010	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3003489	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3003491	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3003493	0.94[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3003500	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3003501	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34861916	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34880762	0.85[EUR][1000 genomes]
rs35389351	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35517171	0.85[EUR][1000 genomes]
rs35756855	0.83[EUR][1000 genomes]
rs3813849	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4236113	0.94[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4236115	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4265033	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4276502	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4286781	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4321822	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4326237	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4336450	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4351263	0.94[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4382260	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4398733	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4437471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4484515	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4489155	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4591854	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4615391	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4712048	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4712049	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4715424	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4715426	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59641455	0.85[EUR][1000 genomes]
rs60035355	0.85[EUR][1000 genomes]
rs6458957	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6458958	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6458959	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6458961	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6458962	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6458965	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458966	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6458969	0.93[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	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6650996	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6899752	0.85[EUR][1000 genomes]
rs6901644	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6920743	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6924025	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925836	0.85[EUR][1000 genomes]
rs6937901	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71555560	0.85[EUR][1000 genomes]
rs742524	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7739965	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7753504	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7754791	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7759946	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs7762883	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7763081	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7763147	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7769893	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7774173	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296719	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296721	0.94[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]
rs9367544	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370235	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370239	0.94[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]
rs9382234	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9382237	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9382250	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9395886	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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:38 , 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	chr6:53693400-53720000	Weak transcription	Left Ventricle	heart
4	chr6:53694000-53708400	Weak transcription	Fetal Thymus	thymus
5	chr6:53695000-53705600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:53695000-53710000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr6:53695000-53719800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:53695000-53743200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:53696400-53708400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:53697200-53718600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr6:53698000-53715600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr6:53699000-53704800	Weak transcription	Fetal Intestine Small	intestine
13	chr6:53699400-53709200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:53700000-53704800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr6:53700400-53709200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:53703000-53705800	Weak transcription	Thymus	Thymus
17	chr6:53703000-53708600	Weak transcription	Gastric	stomach
18	chr6:53703000-53718600	Weak transcription	Pancreas	Pancrea
19	chr6:53703200-53705600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:53703200-53710400	Weak transcription	HUVEC	blood vessel
21	chr6:53703200-53720000	Weak transcription	HSMMtube	muscle
22	chr6:53703200-53720200	Weak transcription	Aorta	Aorta
23	chr6:53703200-53726400	Weak transcription	Fetal Stomach	stomach
24	chr6:53703400-53704800	Enhancers	Brain Germinal Matrix	brain
25	chr6:53703400-53705600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr6:53703400-53707400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:53703400-53710200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr6:53703600-53710600	Weak transcription	Brain Hippocampus Middle	brain
29	chr6:53703800-53717200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr6:53703800-53727600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr6:53704000-53705800	Weak transcription	Esophagus	oesophagus
32	chr6:53704000-53708600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:53704400-53705200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:53704400-53705800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr6:53704400-53707400	Weak transcription	Brain Angular Gyrus	brain
36	chr6:53704400-53710600	Weak transcription	Colon Smooth Muscle	Colon
37	chr6:53704600-53705400	ZNF genes & repeats	HepG2	liver
38	chr6:53704600-53710800	Weak transcription	Rectal Smooth Muscle	rectum

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