Variant report

Variant	rs6041859
Chromosome Location	chr20:13082692-13082693
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1014311	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs1014379	0.95[EUR][1000 genomes]
rs4428077	0.95[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs4814203	0.87[CEU][hapmap]
rs6033621	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs6041860	1.00[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]
rs6041863	0.84[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6041870	1.00[CEU][hapmap];0.81[JPT][hapmap];0.95[EUR][1000 genomes]
rs6041878	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs6041879	0.83[EUR][1000 genomes]
rs6109718	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs720147	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs734261	0.83[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs743092	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs879697	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs879698	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs882301	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	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
14	esv3425983	chr20:13046768-13461834	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13049600-13121800	Weak transcription	Primary T cells from cord blood	blood
2	chr20:13049800-13117600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr20:13053400-13091200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr20:13055200-13092000	Weak transcription	Lung	lung
5	chr20:13055800-13092600	Weak transcription	Aorta	Aorta
6	chr20:13071600-13108000	Weak transcription	Left Ventricle	heart
7	chr20:13071800-13083200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr20:13072600-13100400	Weak transcription	Fetal Stomach	stomach
9	chr20:13073400-13101400	Weak transcription	Fetal Muscle Leg	muscle
10	chr20:13075400-13086400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr20:13075400-13090800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr20:13075400-13096400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr20:13075800-13091000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr20:13075800-13091000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr20:13075800-13092800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr20:13076000-13085600	Weak transcription	Ovary	ovary
17	chr20:13076800-13084200	Weak transcription	Adipose Nuclei	Adipose
18	chr20:13077400-13083200	Weak transcription	Liver	Liver
19	chr20:13078400-13083800	Enhancers	Fetal Intestine Large	intestine
20	chr20:13079800-13083200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr20:13080000-13083200	Weak transcription	Fetal Thymus	thymus
22	chr20:13080000-13084600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr20:13080200-13085600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr20:13080600-13083400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr20:13080600-13085600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr20:13080600-13085600	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr20:13080600-13085600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr20:13080800-13083800	Genic enhancers	HepG2	liver
29	chr20:13080800-13085600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr20:13080800-13085800	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr20:13080800-13102400	Weak transcription	Thymus	Thymus
32	chr20:13081000-13083400	Genic enhancers	Placenta	Placenta
33	chr20:13081000-13083800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr20:13081200-13083400	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr20:13081400-13083600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr20:13081400-13083800	Enhancers	Duodenum Mucosa	Duodenum
37	chr20:13081400-13083800	Genic enhancers	Fetal Intestine Small	intestine
38	chr20:13081600-13083400	Enhancers	Osteobl	bone
39	chr20:13081800-13085600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr20:13081800-13085600	Weak transcription	NHEK	skin
41	chr20:13082000-13083200	Enhancers	NH-A	brain
42	chr20:13082000-13085600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr20:13082200-13083200	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr20:13082200-13083400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr20:13082200-13083600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr20:13082200-13085600	Weak transcription	HMEC	breast
47	chr20:13082400-13083200	Weak transcription	Esophagus	oesophagus
48	chr20:13082400-13083400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr20:13082600-13083000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr20:13082600-13085200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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