Variant report

Variant	rs6041778
Chromosome Location	chr20:13013339-13013340
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11907026	1.00[EUR][1000 genomes]
rs11907467	1.00[EUR][1000 genomes]
rs11908439	1.00[EUR][1000 genomes]
rs11908459	1.00[EUR][1000 genomes]
rs16993615	1.00[EUR][1000 genomes]
rs2876239	0.83[AMR][1000 genomes]
rs3887450	0.83[AMR][1000 genomes]
rs399107	1.00[EUR][1000 genomes]
rs473182	1.00[EUR][1000 genomes]
rs6033571	1.00[EUR][1000 genomes]
rs6033580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6041745	1.00[EUR][1000 genomes]
rs6041746	1.00[EUR][1000 genomes]
rs6041754	1.00[EUR][1000 genomes]
rs6041756	1.00[EUR][1000 genomes]
rs6041773	1.00[EUR][1000 genomes]
rs6041775	1.00[AMR][1000 genomes]
rs6041779	0.83[AMR][1000 genomes]
rs7262471	0.83[AMR][1000 genomes]
rs7271965	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057219	chr20:12729479-13338337	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv912684	chr20:12734299-13311983	Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1067036	chr20:12737436-13338337	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv3488304	chr20:12738054-13341279	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv3488305	chr20:12738054-13341279	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv518184	chr20:12743808-13344672	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1063587	chr20:12756524-13330103	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv544185	chr20:12756524-13330103	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv916296	chr20:12756605-13329940	Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv1067720	chr20:12756725-13329963	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv532513	chr20:12756725-13329963	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv1064901	chr20:12773504-13318421	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv833923	chr20:12904689-13064426	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv833924	chr20:12997093-13189239	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13003400-13015400	Weak transcription	Duodenum Mucosa	Duodenum
2	chr20:13003800-13014600	Weak transcription	Esophagus	oesophagus
3	chr20:13003800-13026400	Weak transcription	Aorta	Aorta
4	chr20:13003800-13049600	Weak transcription	Lung	lung
5	chr20:13004000-13027200	Weak transcription	Pancreas	Pancrea
6	chr20:13004000-13029200	Weak transcription	Ovary	ovary
7	chr20:13006600-13014000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr20:13007800-13014200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr20:13007800-13016200	Weak transcription	Left Ventricle	heart
10	chr20:13008400-13014600	Genic enhancers	Placenta	Placenta
11	chr20:13009600-13015800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr20:13011000-13013400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr20:13011000-13022600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr20:13011200-13018800	Strong transcription	HepG2	liver
15	chr20:13011400-13016800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr20:13011400-13026800	Weak transcription	Stomach Mucosa	stomach
17	chr20:13011600-13014200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr20:13011600-13017800	Weak transcription	NHDF-Ad	bronchial
19	chr20:13011600-13023000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr20:13011800-13014600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr20:13011800-13014600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr20:13011800-13029600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr20:13012000-13018200	Weak transcription	HSMM	muscle
24	chr20:13012200-13013400	Strong transcription	Fetal Intestine Large	intestine
25	chr20:13012400-13018200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr20:13012600-13014000	Weak transcription	NHEK	skin
27	chr20:13012600-13014600	Weak transcription	HMEC	breast
28	chr20:13013000-13013400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr20:13013000-13013600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr20:13013000-13013600	Strong transcription	Liver	Liver
31	chr20:13013200-13013600	Strong transcription	Fetal Intestine Small	intestine

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