Variant report

Variant	rs62217192
Chromosome Location	chr20:25021989-25021990
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VSX1-4	chr20:25021899-25023358	NONHSAT079123

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs6050267	1.00[ASN][1000 genomes]
rs6076312	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083725	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083726	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083727	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083728	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083729	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6115009	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115010	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115011	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115013	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7262168	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7273310	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv912826	chr20:24987787-25071454	Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25012000-25026400	Enhancers	Right Ventricle	heart
2	chr20:25012800-25026400	Enhancers	Brain Angular Gyrus	brain
3	chr20:25013400-25022600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr20:25014000-25026400	Enhancers	Brain Cingulate Gyrus	brain
5	chr20:25014200-25023000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr20:25014200-25026400	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr20:25014400-25025600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr20:25016200-25023800	Enhancers	Stomach Mucosa	stomach
9	chr20:25016200-25024200	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr20:25016200-25024600	Enhancers	Fetal Thymus	thymus
11	chr20:25016400-25024000	Enhancers	Small Intestine	intestine
12	chr20:25016400-25024400	Genic enhancers	Fetal Intestine Small	intestine
13	chr20:25016400-25025800	Enhancers	Fetal Heart	heart
14	chr20:25016600-25022200	Genic enhancers	Fetal Stomach	stomach
15	chr20:25016600-25023800	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr20:25016600-25024600	Enhancers	Pancreas	Pancrea
17	chr20:25016600-25025400	Enhancers	Fetal Muscle Leg	muscle
18	chr20:25016600-25027600	Enhancers	Right Atrium	heart
19	chr20:25016600-25034800	Weak transcription	A549	lung
20	chr20:25017000-25022000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr20:25017000-25022000	Enhancers	Brain Hippocampus Middle	brain
22	chr20:25017000-25026600	Enhancers	Brain Anterior Caudate	brain
23	chr20:25017400-25026400	Enhancers	Brain Substantia Nigra	brain
24	chr20:25017600-25026400	Enhancers	Left Ventricle	heart
25	chr20:25017800-25022400	Enhancers	Esophagus	oesophagus
26	chr20:25017800-25023400	Genic enhancers	Primary T cells fromperipheralblood	blood
27	chr20:25017800-25024400	Enhancers	Lung	lung
28	chr20:25017800-25029000	Genic enhancers	Placenta	Placenta
29	chr20:25017800-25034200	Weak transcription	Fetal Kidney	kidney
30	chr20:25018000-25022600	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr20:25018200-25022200	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr20:25018200-25023000	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr20:25018200-25024800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr20:25018400-25024800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr20:25018600-25024600	Enhancers	Fetal Muscle Trunk	muscle
36	chr20:25018600-25025600	Enhancers	Liver	Liver
37	chr20:25018800-25023200	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr20:25019400-25022000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr20:25019400-25022000	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr20:25019400-25022200	Weak transcription	GM12878-XiMat	blood
41	chr20:25019600-25023400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr20:25019800-25022000	Enhancers	Colon Smooth Muscle	Colon
43	chr20:25019800-25022000	Enhancers	Duodenum Mucosa	Duodenum
44	chr20:25019800-25022600	Strong transcription	Dnd41	blood
45	chr20:25020200-25022000	Strong transcription	Thymus	Thymus
46	chr20:25020200-25024400	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr20:25020200-25026400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr20:25020400-25022800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr20:25020400-25024400	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr20:25020600-25022800	Enhancers	Primary T cells from cord blood	blood

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