Variant report

Variant	rs12908404
Chromosome Location	chr15:29848687-29848688
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12898464	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905831	0.86[EUR][1000 genomes]
rs12913593	0.86[EUR][1000 genomes]
rs4780239	0.93[ASN][1000 genomes]
rs779	0.83[EUR][1000 genomes]
rs8029317	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8036248	1.00[ASN][1000 genomes]
rs8042563	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs898253	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9888716	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456736	chr15:29327352-30208654	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers 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	nsv568675	chr15:29327352-30208654	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer 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
3	nsv903747	chr15:29361126-30008977	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv3364436	chr15:29459739-29853229	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv995038	chr15:29744279-30366124	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv832943	chr15:29788334-29924284	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv456737	chr15:29812777-29875999	Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv568680	chr15:29812777-29875999	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv456738	chr15:29812777-29889806	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv1038495	chr15:29825859-30351687	Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
11	nsv542293	chr15:29825859-30351687	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
12	nsv974491	chr15:29848503-29849278	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12908404	HBII-52-28	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:29842000-29849000	Weak transcription	Pancreas	Pancrea
2	chr15:29846400-29849200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr15:29848000-29859200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:29848200-29849400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr15:29848200-29861200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr15:29848400-29848800	Enhancers	Fetal Lung	lung
7	chr15:29848400-29849000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr15:29848400-29849000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:29848400-29849200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr15:29848400-29849400	Enhancers	Ovary	ovary
11	chr15:29848600-29849000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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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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