Variant report

Variant	rs2055858
Chromosome Location	chr15:45314268-45314269
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11070439	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11635836	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12902552	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12902975	0.81[ASN][1000 genomes]
rs12903068	0.83[ASN][1000 genomes]
rs12916850	0.82[ASN][1000 genomes]
rs16976876	0.85[ASN][1000 genomes]
rs1720689	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs199334	0.90[EUR][1000 genomes]
rs2217932	0.87[ASN][1000 genomes]
rs270822	0.85[EUR][1000 genomes]
rs34428536	0.94[ASN][1000 genomes]
rs35881035	0.96[ASN][1000 genomes]
rs3759890	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3858900	0.94[ASN][1000 genomes]
rs58751943	0.83[ASN][1000 genomes]
rs67352586	0.84[ASN][1000 genomes]
rs71405285	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71478352	0.96[ASN][1000 genomes]
rs7169807	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72722052	0.95[ASN][1000 genomes]
rs8182070	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758380	chr15:44968868-45422842	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	esv2760029	chr15:44968868-45422842	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
4	esv2757599	chr15:45100852-45383620	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv1048317	chr15:45152371-45326205	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv904184	chr15:45248787-45314764	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2055858	RP11-109D20.2	cis	Skin Sun Exposed Lower leg	GTEx
rs2055858	CTD-2008A1.2	cis	Skin Sun Exposed Lower leg	GTEx
rs2055858	SORD	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45312600-45314800	Enhancers	Stomach Mucosa	stomach
2	chr15:45312800-45314400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:45313200-45314400	Weak transcription	Liver	Liver
4	chr15:45313200-45314800	Enhancers	HepG2	liver
5	chr15:45313400-45314600	Weak transcription	Gastric	stomach
6	chr15:45313400-45314600	Weak transcription	Pancreas	Pancrea
7	chr15:45313600-45314600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr15:45313600-45314600	Enhancers	Duodenum Mucosa	Duodenum
9	chr15:45313800-45314600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr15:45313800-45314800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:45314000-45314400	Enhancers	Hela-S3	cervix
12	chr15:45314000-45314600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:45314000-45314600	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr15:45314200-45314600	Enhancers	Primary T cells fromperipheralblood	blood
15	chr15:45314200-45314600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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