Variant report

Variant	rs28954069
Chromosome Location	chr2:113742314-113742315
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12328178	1.00[AMR][1000 genomes]
rs28954070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28954073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28954368	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6707930	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73955290	1.00[AMR][1000 genomes]
rs9973878	0.99[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	nsv532471	chr2:113682449-113862981	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1007254	chr2:113726982-113887782	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer 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	12 gene(s)	inside rSNPs	diseases
4	nsv535894	chr2:113726982-113887782	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113736000-113747400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:113737400-113742400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:113737600-113742600	Weak transcription	Thymus	Thymus
4	chr2:113738400-113742400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:113738400-113742400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr2:113738600-113742400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr2:113742000-113743800	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr2:113742000-113744000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr2:113742200-113743800	Enhancers	Fetal Thymus	thymus
10	chr2:113742200-113744000	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr2:113742200-113744000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr2:113742200-113744000	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr2:113742200-113744200	Enhancers	Primary T cells from cord blood	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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