Variant report

Variant	rs16903778
Chromosome Location	chr5:15015736-15015737
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:15014377..15017867-chr5:15019671..15021896,3	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10044822	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10044904	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10044907	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10044908	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10067400	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10513194	0.89[ASN][1000 genomes]
rs10513195	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11744215	0.89[ASN][1000 genomes]
rs16903773	0.93[ASN][1000 genomes]
rs57219003	0.88[ASN][1000 genomes]
rs58317516	1.00[EUR][1000 genomes]
rs62356077	0.86[ASN][1000 genomes]
rs6859541	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6864877	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6867275	0.93[ASN][1000 genomes]
rs6877954	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6878138	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6878288	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6878430	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73053946	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73053947	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73053951	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73053957	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7341022	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7341067	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7341168	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9312876	0.89[ASN][1000 genomes]
rs9686327	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv530221	chr5:14859687-15364470	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv432717	chr5:14887400-15126500	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1017579	chr5:14888997-15194335	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv461982	chr5:14943456-15044842	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv597262	chr5:14943456-15044842	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv470991	chr5:14949696-15022112	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv524142	chr5:14986700-15018537	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:15009400-15020800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:15009800-15021000	Weak transcription	Aorta	Aorta
3	chr5:15013600-15016400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr5:15013600-15016600	Enhancers	Osteobl	bone
5	chr5:15013800-15015800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr5:15013800-15016200	Enhancers	Fetal Heart	heart
7	chr5:15014200-15016400	Enhancers	HSMMtube	muscle
8	chr5:15015000-15017000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:15015200-15015800	Enhancers	HepG2	liver
10	chr5:15015200-15015800	Weak transcription	HMEC	breast
11	chr5:15015200-15016000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr5:15015200-15018600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr5:15015200-15020400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr5:15015200-15021200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr5:15015600-15016600	Enhancers	A549	lung
16	chr5:15015600-15020800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:15015600-15021000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr5:15015600-15021000	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links