Variant report

Variant	rs7271177
Chromosome Location	chr20:52604054-52604055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12329598	0.87[AFR][1000 genomes]
rs16998695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16998697	0.87[AMR][1000 genomes]
rs2276493	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2870302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56254566	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56358601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6022891	0.89[AMR][1000 genomes]
rs60878965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6097708	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6097710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6097712	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6097717	0.87[AFR][1000 genomes]
rs6097720	0.87[AFR][1000 genomes]
rs73914443	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73914470	0.80[AFR][1000 genomes]
rs740373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52566400-52644800	Weak transcription	Gastric	stomach
2	chr20:52581200-52610600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr20:52601400-52612400	Weak transcription	Brain Angular Gyrus	brain
4	chr20:52601400-52612400	Weak transcription	Brain Anterior Caudate	brain
5	chr20:52601600-52606000	Weak transcription	Brain Hippocampus Middle	brain
6	chr20:52601600-52606000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr20:52601800-52609800	Weak transcription	Brain Substantia Nigra	brain
8	chr20:52601800-52612400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr20:52601800-52630800	Weak transcription	Stomach Mucosa	stomach
10	chr20:52602000-52604800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr20:52602000-52608800	Weak transcription	Fetal Stomach	stomach
12	chr20:52602800-52608800	Weak transcription	HSMMtube	muscle
13	chr20:52602800-52610000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr20:52603800-52604400	Enhancers	Rectal Mucosa Donor 29	rectum

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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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