Variant report

Variant	rs2293544
Chromosome Location	chr2:96603129-96603130
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPAT2-4	chr2:96602559-96604956	NONHSAT072522

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs35056623	0.82[EUR][1000 genomes]
rs4146063	0.96[EUR][1000 genomes]
rs59534363	0.96[EUR][1000 genomes]
rs72492169	0.96[EUR][1000 genomes]
rs72823940	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3416818	chr2:96072529-96680708	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS 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	43 gene(s)	inside rSNPs	diseases
2	nsv874660	chr2:96091132-96669134	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv516044	chr2:96150959-96683378	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv1003371	chr2:96326106-96684876	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS 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	17 gene(s)	inside rSNPs	diseases
5	nsv874666	chr2:96370571-96691125	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent Enhancer 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
6	nsv428054	chr2:96438238-96627125	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv961832	chr2:96453677-96671971	Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv834304	chr2:96493545-96667472	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv508154	chr2:96534336-96609925	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1004486	chr2:96544604-96684876	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv874669	chr2:96547820-96691125	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv818073	chr2:96554851-96683378	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	esv1840487	chr2:96582807-96836512	Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
14	esv1811444	chr2:96583510-96631703	Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases
15	esv1810451	chr2:96583710-96622087	ZNF genes & repeats Weak transcription Strong transcription Enhancers	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases
16	esv1812776	chr2:96584211-96622287	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases
17	esv1805585	chr2:96589999-96629291	Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases
18	esv21137	chr2:96591462-96623415	Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases
19	nsv820407	chr2:96591462-96623415	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases
20	esv14492	chr2:96591462-96647854	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases
21	esv3391744	chr2:96592125-96609923	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
22	esv3347102	chr2:96593525-96610023	Weak transcription ZNF genes & repeats Enhancers Strong transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96502800-96616600	Weak transcription	Fetal Stomach	stomach
2	chr2:96556200-96645000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr2:96556400-96628600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:96556400-96645000	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr2:96557400-96656800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr2:96574200-96629600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:96574600-96627600	Weak transcription	HSMM	muscle
8	chr2:96576800-96616200	Weak transcription	Brain Germinal Matrix	brain
9	chr2:96577800-96603400	Weak transcription	Osteobl	bone
10	chr2:96577800-96647800	Weak transcription	NHDF-Ad	bronchial
11	chr2:96577800-96651000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:96577800-96656600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:96578000-96645000	Weak transcription	NH-A	brain
14	chr2:96581400-96617000	Weak transcription	Pancreas	Pancrea
15	chr2:96582000-96605800	Weak transcription	Fetal Intestine Small	intestine
16	chr2:96582800-96656400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:96584000-96624600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:96584400-96621600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr2:96585200-96649000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr2:96585400-96616600	Weak transcription	Fetal Muscle Leg	muscle
21	chr2:96585600-96615400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr2:96585600-96627400	Weak transcription	Left Ventricle	heart
23	chr2:96586000-96657200	Weak transcription	Ovary	ovary
24	chr2:96587600-96607800	Weak transcription	Aorta	Aorta
25	chr2:96587800-96656600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr2:96588200-96649000	Weak transcription	Fetal Intestine Large	intestine
27	chr2:96589000-96616000	Weak transcription	Fetal Lung	lung
28	chr2:96589000-96631200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr2:96589000-96645400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr2:96589200-96605800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr2:96589400-96607000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:96591000-96610200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:96591200-96616200	Weak transcription	Fetal Thymus	thymus
34	chr2:96593000-96610000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:96593600-96616200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:96593600-96645000	Weak transcription	Adipose Nuclei	Adipose
37	chr2:96594400-96617600	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr2:96594600-96623800	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr2:96594800-96610000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr2:96595600-96610200	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr2:96598200-96610000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr2:96598400-96606000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:96600400-96604200	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr2:96600600-96657200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:96600800-96603400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:96600800-96610000	Weak transcription	Dnd41	blood
47	chr2:96600800-96610400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr2:96600800-96617600	Weak transcription	Fetal Brain Male	brain
49	chr2:96600800-96621400	Weak transcription	A549	lung
50	chr2:96600800-96625600	Weak transcription	Rectal Mucosa Donor 29	rectum

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