Variant report

Variant	rs2680653
Chromosome Location	chr3:53695716-53695717
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1356657	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1356658	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1401493	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1401498	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2612017	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2612021	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2633711	1.00[AMR][1000 genomes]
rs2633712	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2633733	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2680655	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2680667	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36003262	0.85[AFR][1000 genomes]
rs6780679	1.00[AMR][1000 genomes]
rs6798837	1.00[AMR][1000 genomes]
rs72976490	1.00[AMR][1000 genomes]
rs746487	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7614320	0.89[AFR][1000 genomes]
rs7630968	1.00[AMR][1000 genomes]
rs898414	0.89[AFR][1000 genomes]
rs9311508	0.85[AFR][1000 genomes]
rs9845102	0.85[AFR][1000 genomes]
rs9857905	1.00[AMR][1000 genomes]
rs9875160	0.85[AFR][1000 genomes]
rs9875748	1.00[AMR][1000 genomes]
rs9878618	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53677600-53700000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr3:53683200-53744200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:53684800-53698600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr3:53685800-53695800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:53689600-53707400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:53692000-53707600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:53693600-53697600	ZNF genes & repeats	Liver	Liver
8	chr3:53694200-53695800	Genic enhancers	Fetal Lung	lung
9	chr3:53694200-53699000	Strong transcription	Fetal Intestine Small	intestine
10	chr3:53694200-53699200	Strong transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:53694200-53700400	Strong transcription	Fetal Intestine Large	intestine
12	chr3:53694400-53701000	Weak transcription	Fetal Kidney	kidney
13	chr3:53694800-53696000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
14	chr3:53695000-53697400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr3:53695200-53696000	Weak transcription	Fetal Stomach	stomach

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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