Variant report

Variant	rs28904021
Chromosome Location	chr2:234985376-234985377
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10174012	1.00[EUR][1000 genomes]
rs10177507	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16850570	1.00[EUR][1000 genomes]
rs28901651	1.00[EUR][1000 genomes]
rs28901656	1.00[EUR][1000 genomes]
rs28903676	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28903677	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28903679	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28903686	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28903693	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28903971	1.00[EUR][1000 genomes]
rs28903986	0.83[AMR][1000 genomes]
rs28903987	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28903992	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28903998	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28948682	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73113209	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73124598	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73124600	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73124601	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73999215	1.00[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	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv834571	chr2:234929288-235110332	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv998149	chr2:234978261-235086951	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 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	chr2:234972600-234985600	Strong transcription	Liver	Liver
2	chr2:234984000-234985600	Enhancers	Gastric	stomach
3	chr2:234984000-234987000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:234984200-234987000	Enhancers	Primary T cells fromperipheralblood	blood
5	chr2:234984400-234985600	Bivalent Enhancer	HepG2	liver
6	chr2:234984400-234987200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr2:234984600-234985400	Enhancers	Duodenum Mucosa	Duodenum
8	chr2:234984800-234985600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr2:234984800-234985600	Enhancers	Pancreas	Pancrea
10	chr2:234984800-234985600	Enhancers	Stomach Mucosa	stomach
11	chr2:234984800-234985600	Enhancers	Thymus	Thymus
12	chr2:234984800-234986000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:234984800-234987200	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr2:234984800-234987400	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr2:234985000-234985600	Enhancers	Fetal Thymus	thymus
16	chr2:234985000-234986000	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr2:234985200-234985600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
18	chr2:234985200-234986600	Enhancers	Primary T cells from cord blood	blood
19	chr2:234985200-234986600	Enhancers	Primary T helper cells fromperipheralblood	blood

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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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