Variant report

Variant	rs2820966
Chromosome Location	chr1:47906338-47906339
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1765156	0.83[AFR][1000 genomes]
rs2622916	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs472993	0.89[AFR][1000 genomes]
rs479363	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4926868	0.89[AFR][1000 genomes]
rs495482	0.83[AFR][1000 genomes]
rs506329	0.89[AFR][1000 genomes]
rs522768	0.89[AFR][1000 genomes]
rs527133	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs527430	0.89[AFR][1000 genomes]
rs557101	0.83[AFR][1000 genomes]
rs567097	1.00[AMR][1000 genomes]
rs6665542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6676787	1.00[AMR][1000 genomes]
rs9436456	0.89[AFR][1000 genomes]
rs9436902	0.83[AFR][1000 genomes];1.00[AMR][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	nsv871961	chr1:47875627-47912628	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534957	chr1:47882277-47907965	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1001779	chr1:47884229-48111485	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv871299	chr1:47889417-48057890	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47901400-47908000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
2	chr1:47902800-47906400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:47902800-47906600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
4	chr1:47904400-47906800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:47904600-47906600	Bivalent/Poised TSS	Small Intestine	intestine
6	chr1:47904800-47906600	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
7	chr1:47904800-47910000	Weak transcription	Pancreas	Pancrea
8	chr1:47905000-47906600	Weak transcription	Aorta	Aorta
9	chr1:47905000-47906800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
10	chr1:47905200-47906600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
11	chr1:47905200-47907400	Weak transcription	Right Atrium	heart
12	chr1:47905200-47907800	Bivalent/Poised TSS	Fetal Kidney	kidney
13	chr1:47905400-47906600	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
14	chr1:47905400-47906600	Bivalent Enhancer	Fetal Intestine Large	intestine
15	chr1:47905600-47908600	Active TSS	Colonic Mucosa	Colon
16	chr1:47906000-47906400	Bivalent Enhancer	Duodenum Mucosa	Duodenum
17	chr1:47906000-47906600	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:47906000-47907400	Active TSS	Rectal Mucosa Donor 31	rectum
19	chr1:47906000-47910000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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