Variant report

Variant	rs1014379
Chromosome Location	chr20:13094935-13094936
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ISM1-3	chr20:13093137-13095336	NONHSAT078679

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1014311	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4375935	0.88[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs4428077	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4814203	0.94[JPT][hapmap]
rs6033621	0.81[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6041859	0.95[EUR][1000 genomes]
rs6041860	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6041863	0.82[CHB][hapmap];0.89[JPT][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6041870	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6041878	0.88[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6041879	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6109718	0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs720147	0.80[EUR][1000 genomes]
rs734261	0.88[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs743092	0.94[CHB][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs879697	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs879698	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs882301	0.81[AMR][1000 genomes];0.95[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	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:36 , 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	chr20:13071600-13108000	Weak transcription	Left Ventricle	heart
4	chr20:13072600-13100400	Weak transcription	Fetal Stomach	stomach
5	chr20:13073400-13101400	Weak transcription	Fetal Muscle Leg	muscle
6	chr20:13075400-13096400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr20:13080800-13102400	Weak transcription	Thymus	Thymus
8	chr20:13083600-13095800	Weak transcription	Esophagus	oesophagus
9	chr20:13083600-13114600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr20:13086200-13107600	Weak transcription	NHEK	skin
11	chr20:13086600-13123200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr20:13087000-13100400	Weak transcription	Fetal Lung	lung
13	chr20:13087000-13108200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr20:13087200-13101600	Strong transcription	Placenta	Placenta
15	chr20:13087800-13107200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr20:13088800-13103000	Strong transcription	Fetal Intestine Large	intestine
17	chr20:13091800-13127800	Weak transcription	Fetal Kidney	kidney
18	chr20:13092400-13096200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr20:13092600-13100400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr20:13092800-13095800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr20:13092800-13100000	Strong transcription	HepG2	liver
22	chr20:13093000-13144600	Weak transcription	Pancreas	Pancrea
23	chr20:13093200-13102600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr20:13093200-13106800	Weak transcription	Ovary	ovary
25	chr20:13093400-13108000	Weak transcription	Aorta	Aorta
26	chr20:13093400-13111000	Weak transcription	Lung	lung
27	chr20:13093600-13098000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr20:13093600-13099200	Weak transcription	Adipose Nuclei	Adipose
29	chr20:13093800-13098400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr20:13094200-13097400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr20:13094200-13103400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr20:13094600-13095800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr20:13094600-13114400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr20:13094800-13096600	Weak transcription	Fetal Intestine Small	intestine
35	chr20:13094800-13098200	Weak transcription	Liver	Liver
36	chr20:13094800-13101800	Weak transcription	Duodenum Mucosa	Duodenum

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