Variant report

Variant	rs3798609
Chromosome Location	chr6:119536887-119536888
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1104741	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11153798	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11153801	0.84[ASN][1000 genomes]
rs11153802	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11755686	0.84[ASN][1000 genomes]
rs11962211	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12207164	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12211868	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1295386	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs1408491	0.93[ASN][1000 genomes]
rs1408492	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1408493	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1555683	0.85[ASN][1000 genomes]
rs195046	0.96[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs195051	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs195062	0.84[EUR][1000 genomes]
rs195063	0.84[CHB][hapmap]
rs195071	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs195078	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs195081	0.85[CHB][hapmap]
rs195088	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs195091	0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2064160	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2142890	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2267672	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2267673	0.88[AFR][1000 genomes]
rs2267674	0.88[AFR][1000 genomes]
rs2267675	0.88[AFR][1000 genomes]
rs2299878	0.96[YRI][hapmap]
rs2299879	1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs2299881	0.86[ASN][1000 genomes]
rs2357162	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2357163	0.87[ASN][1000 genomes]
rs3798616	0.87[ASN][1000 genomes]
rs3822997	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4945633	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6569060	0.83[CEU][hapmap]
rs6569061	0.92[CEU][hapmap]
rs6569063	0.85[ASN][1000 genomes]
rs6569074	0.85[JPT][hapmap]
rs6933914	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7357047	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7357048	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs763293	0.87[ASN][1000 genomes]
rs7775421	0.82[CEU][hapmap]
rs9320684	1.00[CEU][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9385068	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489624	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9489625	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489627	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9489628	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9489633	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9489654	0.83[ASN][1000 genomes]
rs980818	0.83[CEU][hapmap]
rs998194	0.83[CEU][hapmap]

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	nsv1025995	chr6:119407742-119709548	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv886570	chr6:119450888-119600556	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1017507	chr6:119465981-119664949	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1034992	chr6:119512657-119540895	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119494600-119547400	Weak transcription	Esophagus	oesophagus
2	chr6:119503400-119539800	Weak transcription	Gastric	stomach
3	chr6:119519200-119558400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr6:119524800-119537000	Weak transcription	Pancreas	Pancrea
5	chr6:119524800-119539000	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr6:119524800-119558400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:119525400-119537000	Weak transcription	Right Ventricle	heart
8	chr6:119525400-119537400	Weak transcription	Brain Anterior Caudate	brain
9	chr6:119525400-119548600	Weak transcription	Aorta	Aorta
10	chr6:119525400-119556000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr6:119525400-119558400	Weak transcription	Small Intestine	intestine
12	chr6:119525800-119537000	Weak transcription	Left Ventricle	heart
13	chr6:119525800-119554200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr6:119525800-119555800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:119526000-119538800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr6:119526000-119555200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:119526000-119558400	Weak transcription	Placenta	Placenta
18	chr6:119526200-119558400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr6:119528600-119551200	Weak transcription	Primary B cells from cord blood	blood
20	chr6:119530000-119537000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr6:119530000-119537200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:119531200-119552000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr6:119531400-119537200	Weak transcription	Right Atrium	heart
24	chr6:119531600-119558400	Weak transcription	NHLF	lung
25	chr6:119532200-119537200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:119535400-119538400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:119535600-119538200	Enhancers	Fetal Lung	lung
28	chr6:119535800-119537600	Enhancers	Adipose Nuclei	Adipose
29	chr6:119536000-119537000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:119536000-119537000	Weak transcription	Ovary	ovary
31	chr6:119536200-119537000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:119536200-119538400	Enhancers	Liver	Liver
33	chr6:119536400-119537200	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr6:119536400-119537400	Enhancers	Fetal Intestine Large	intestine
35	chr6:119536400-119537400	Enhancers	Fetal Intestine Small	intestine
36	chr6:119536400-119537400	Enhancers	Fetal Stomach	stomach
37	chr6:119536400-119538200	Enhancers	Colon Smooth Muscle	Colon
38	chr6:119536400-119540000	Genic enhancers	HepG2	liver
39	chr6:119536600-119537200	Genic enhancers	K562	blood
40	chr6:119536600-119537600	Strong transcription	Primary hematopoietic stem cells	blood
41	chr6:119536600-119538200	Enhancers	Fetal Heart	heart
42	chr6:119536800-119541600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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