Variant report

Variant	rs28819453
Chromosome Location	chr2:113366965-113366966
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs12987250	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13025131	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17586834	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17587043	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17647292	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34015418	0.90[EUR][1000 genomes]
rs35670704	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36082214	0.91[EUR][1000 genomes]
rs3980072	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3980073	0.86[EUR][1000 genomes]
rs3980074	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6737981	0.93[EUR][1000 genomes]
rs6743603	0.86[EUR][1000 genomes]
rs71414685	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7566777	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7607685	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7607817	1.00[AMR][1000 genomes];0.93[EUR][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	nsv874877	chr2:113287964-113382054	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs28819453	AC079922.3	cis	Thyroid	GTEx
rs28819453	AC079922.3	cis	Artery Aorta	GTEx
rs28819453	AC079922.3	cis	Muscle Skeletal	GTEx
rs28819453	AC079922.3	cis	Esophagus Mucosa	GTEx
rs28819453	AC079922.3	cis	Artery Tibial	GTEx
rs28819453	AC079922.3	cis	lung	GTEx
rs28819453	AC079922.3	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113346800-113374600	Weak transcription	Ovary	ovary
2	chr2:113348600-113383600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:113349000-113384000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr2:113357000-113371800	Weak transcription	Gastric	stomach
5	chr2:113357800-113375200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:113357800-113384200	Weak transcription	Pancreas	Pancrea
7	chr2:113358000-113371800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr2:113358000-113384000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:113359600-113371800	Weak transcription	Brain Germinal Matrix	brain
10	chr2:113359800-113372000	Weak transcription	Fetal Brain Female	brain
11	chr2:113364600-113368000	Weak transcription	Stomach Mucosa	stomach
12	chr2:113364600-113370800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:113364600-113372800	Weak transcription	Fetal Stomach	stomach
14	chr2:113365600-113372000	Weak transcription	Brain Anterior Caudate	brain

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Input of quick search could be:

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

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