Variant report

Variant	rs11900781
Chromosome Location	chr2:98565761-98565762
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VWA3B-3	chr2:98565165-98565970	expReg_chr2_7491_+

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11892146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11895466	1.00[AMR][1000 genomes]
rs11898394	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11900903	1.00[AMR][1000 genomes]
rs11903844	0.81[AFR][1000 genomes]
rs1503201	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1503203	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022209	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022289	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022557	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022726	1.00[AMR][1000 genomes]
rs17022736	1.00[AMR][1000 genomes]
rs17025339	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2309318	0.81[AFR][1000 genomes]
rs35774346	0.85[AFR][1000 genomes]
rs56065241	1.00[AMR][1000 genomes]
rs57434542	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58187838	1.00[AMR][1000 genomes]
rs60828800	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60885334	1.00[AMR][1000 genomes]
rs61712471	1.00[AMR][1000 genomes]
rs6543226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6726775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6734701	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6736475	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6737992	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6742955	0.81[AFR][1000 genomes]
rs6746457	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942824	1.00[AMR][1000 genomes]
rs72942830	1.00[AMR][1000 genomes]
rs72942834	1.00[AMR][1000 genomes]
rs72942836	1.00[AMR][1000 genomes]
rs72942856	1.00[AMR][1000 genomes]
rs72942862	1.00[AMR][1000 genomes]
rs72942871	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942872	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942876	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942885	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942894	0.82[AFR][1000 genomes]
rs72942896	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942898	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944808	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944812	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944813	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944818	0.94[AFR][1000 genomes]
rs72944825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946409	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946410	0.81[AFR][1000 genomes]
rs72946417	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946421	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946425	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946431	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946447	1.00[AMR][1000 genomes]
rs72946448	1.00[AMR][1000 genomes]
rs72946453	1.00[AMR][1000 genomes]
rs7579764	1.00[AMR][1000 genomes]
rs9308889	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh 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
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1013416	chr2:98472701-98688729	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv960975	chr2:98562321-98567447	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98553200-98565800	Weak transcription	Small Intestine	intestine
2	chr2:98553800-98565800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr2:98554000-98565800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:98554000-98570200	Weak transcription	Primary B cells from cord blood	blood
5	chr2:98559800-98567800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr2:98560200-98566400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:98561400-98566800	Weak transcription	HSMMtube	muscle
8	chr2:98561800-98565800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr2:98561800-98566800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:98561800-98570200	Weak transcription	Primary T cells from cord blood	blood
11	chr2:98562000-98567400	Weak transcription	Brain Substantia Nigra	brain
12	chr2:98562200-98566200	Weak transcription	HSMM	muscle
13	chr2:98562200-98570400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr2:98562400-98569200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:98562600-98566400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:98562600-98566400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:98562600-98566400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:98562600-98566400	Weak transcription	NHDF-Ad	bronchial
19	chr2:98562600-98566400	Weak transcription	Osteobl	bone
20	chr2:98562600-98566600	Weak transcription	NHEK	skin
21	chr2:98562600-98566800	Weak transcription	Right Ventricle	heart
22	chr2:98562600-98566800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr2:98562600-98567200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr2:98562600-98567600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr2:98562600-98567800	Weak transcription	Liver	Liver
26	chr2:98562600-98568000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr2:98562600-98570000	Weak transcription	Fetal Intestine Small	intestine
28	chr2:98562600-98570200	Weak transcription	Fetal Lung	lung
29	chr2:98562800-98567800	Weak transcription	Right Atrium	heart
30	chr2:98563000-98565800	Weak transcription	NHLF	lung
31	chr2:98563000-98566800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr2:98563200-98565800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:98563200-98567000	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr2:98563200-98567200	Weak transcription	Stomach Mucosa	stomach
35	chr2:98563400-98570600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr2:98563600-98566800	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr2:98563600-98569600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr2:98563600-98589200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:98564400-98566000	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr2:98564400-98566200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:98564600-98567400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr2:98564600-98567600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:98564600-98580600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr2:98565000-98566200	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr2:98565200-98566000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr2:98565400-98566000	Enhancers	Primary B cells from peripheral blood	blood
47	chr2:98565400-98566000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:98565400-98566000	ZNF genes & repeats	GM12878-XiMat	blood
49	chr2:98565400-98569200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:98565600-98565800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell

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