Variant report

Variant	rs56412571
Chromosome Location	chr2:56184558-56184559
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EFEMP1-1	chr2:56183727-56185924	NONHSAT070812

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10518794	1.00[EUR][1000 genomes]
rs13429887	0.84[EUR][1000 genomes]
rs14282	0.84[EUR][1000 genomes]
rs55676306	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55749412	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55811442	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55845766	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55886642	0.84[EUR][1000 genomes]
rs55912959	0.85[EUR][1000 genomes]
rs56058144	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56195925	0.85[EUR][1000 genomes]
rs56309449	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72811719	0.84[EUR][1000 genomes]
rs72813864	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72813868	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72813873	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72813875	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72813877	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72813878	0.85[EUR][1000 genomes]
rs72813879	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72813880	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72813884	0.85[EUR][1000 genomes]
rs72813888	0.85[EUR][1000 genomes]
rs72813889	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72813894	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72813900	0.89[AMR][1000 genomes]
rs72813901	0.89[AMR][1000 genomes]
rs72813902	0.89[AMR][1000 genomes]
rs72815903	0.89[AMR][1000 genomes]
rs72815905	0.89[AMR][1000 genomes]
rs72815906	0.89[AMR][1000 genomes]
rs72815909	0.89[AMR][1000 genomes]
rs72815910	0.89[AMR][1000 genomes]
rs72815912	0.89[AMR][1000 genomes]
rs7600678	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv874161	chr2:56154316-56203798	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	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
4	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

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56171000-56185000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:56178000-56185200	Weak transcription	Right Atrium	heart
3	chr2:56180000-56188800	Weak transcription	Colon Smooth Muscle	Colon
4	chr2:56182400-56185200	Weak transcription	NH-A	brain
5	chr2:56182600-56185000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr2:56182600-56185200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:56182600-56185400	Weak transcription	Fetal Lung	lung
8	chr2:56183800-56185200	Enhancers	A549	lung
9	chr2:56183800-56185200	Enhancers	Osteobl	bone
10	chr2:56183800-56186400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:56183800-56186600	Enhancers	Placenta Amnion	Placenta Amnion
12	chr2:56184000-56185200	Enhancers	Hela-S3	cervix
13	chr2:56184000-56186000	Weak transcription	Ovary	ovary
14	chr2:56184000-56186400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:56184200-56185800	Enhancers	Adipose Nuclei	Adipose
16	chr2:56184200-56186600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:56184400-56184800	Weak transcription	Placenta	Placenta
18	chr2:56184400-56185200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:56184400-56185200	Enhancers	NHEK	skin
20	chr2:56184400-56185800	Enhancers	Pancreas	Pancrea
21	chr2:56184400-56186600	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr2:56184400-56186600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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