Variant report

Variant	rs13430597
Chromosome Location	chr2:56411993-56411994
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EFEMP1-3	chr2:56411759-56412043	ENSG00000233251.3

Extended variants
information (count: 13 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13415415	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13415516	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13415520	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13415535	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13415624	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757799	chr2:56178439-56472394	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2759051	chr2:56178439-56472394	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
3	nsv874162	chr2:56255832-56480571	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv874169	chr2:56383762-56473480	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv2762648	chr2:56386656-56422448	Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv3411625	chr2:56409873-56412421	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3442902	chr2:56410148-56412896	Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv3330480	chr2:56410673-56413221	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56410400-56412800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:56410600-56412000	Bivalent/Poised TSS	HepG2	liver
3	chr2:56410600-56412000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
4	chr2:56410600-56412600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
5	chr2:56410600-56412600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:56410600-56412800	Active TSS	HSMM	muscle
7	chr2:56410600-56413000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
8	chr2:56410600-56413000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:56410600-56413000	Active TSS	Muscle Satellite Cultured Cells	--
10	chr2:56410600-56413000	Active TSS	HSMMtube	muscle
11	chr2:56410600-56413200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
12	chr2:56410600-56413200	Active TSS	Brain Angular Gyrus	brain
13	chr2:56410600-56413400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
14	chr2:56410600-56413400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:56410600-56413400	Active TSS	Brain Hippocampus Middle	brain
16	chr2:56410600-56413400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr2:56410600-56413600	Active TSS	Psoas Muscle	Psoas
18	chr2:56410600-56413600	Active TSS	Right Atrium	heart
19	chr2:56410800-56412000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
20	chr2:56410800-56412000	Active TSS	Placenta Amnion	Placenta Amnion
21	chr2:56410800-56412200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
22	chr2:56410800-56412200	Active TSS	Brain Anterior Caudate	brain
23	chr2:56410800-56412200	Active TSS	Colon Smooth Muscle	Colon
24	chr2:56410800-56412200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
25	chr2:56410800-56412200	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
26	chr2:56410800-56412200	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
27	chr2:56410800-56412200	Active TSS	Rectal Smooth Muscle	rectum
28	chr2:56410800-56412400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:56410800-56412400	Active TSS	H9 Cell Line	embryonic stem cell
30	chr2:56410800-56412400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:56410800-56412400	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr2:56410800-56412400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr2:56410800-56412400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
34	chr2:56410800-56412600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
35	chr2:56410800-56412600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
36	chr2:56410800-56412600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:56410800-56412600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:56410800-56412600	Active TSS	Gastric	stomach
39	chr2:56410800-56412600	Bivalent/Poised TSS	A549	lung
40	chr2:56410800-56412600	Active TSS	HUVEC	blood vessel
41	chr2:56410800-56413000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:56410800-56413000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
43	chr2:56410800-56413000	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:56410800-56413000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr2:56410800-56413000	Active TSS	Brain Substantia Nigra	brain
46	chr2:56410800-56413000	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
47	chr2:56410800-56413000	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr2:56410800-56413000	Bivalent/Poised TSS	Osteobl	bone
49	chr2:56410800-56413200	Active TSS	Brain Cingulate Gyrus	brain
50	chr2:56410800-56413400	Active TSS	Left Ventricle	heart

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