Variant report

Variant	rs4788534
Chromosome Location	chr16:71252571-71252572
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:71250057..71252959-chr16:71321455..71323555,3	MCF-7	breast:
2	chr16:71199464..71201257-chr16:71252369..71255070,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180917	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1155052	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1155054	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12051093	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12448046	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12449210	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12933427	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13332757	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1424134	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1424136	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1424137	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1557761	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1559420	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1895528	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2042423	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2081253	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2098746	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2158102	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28663037	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2883938	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35645515	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3743954	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3785346	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3902443	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4636918	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4788529	0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4788536	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4788766	0.93[AFR][1000 genomes]
rs6499489	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7193051	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7498840	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs757106	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs764600	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8052442	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8063809	0.86[ASN][1000 genomes]
rs987958	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9924525	0.94[ASN][1000 genomes]
rs9928164	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9930115	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9932494	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9934510	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9936084	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9936905	0.92[ASN][1000 genomes]
rs9939194	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9939485	0.83[ASN][1000 genomes]
rs9939836	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9940569	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758429	chr16:70807122-71316983	Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	esv2758653	chr16:70807122-71316983	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv1060754	chr16:71008303-71276778	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv949461	chr16:71196153-71579711	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv482374	chr16:71228600-71401617	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 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	chr16:71250800-71253200	Enhancers	Fetal Brain Male	brain
2	chr16:71251000-71252800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr16:71251000-71264200	Weak transcription	Pancreas	Pancrea
4	chr16:71251400-71252600	Enhancers	H1 Cell Line	embryonic stem cell
5	chr16:71251600-71252800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr16:71251600-71253200	Enhancers	Brain Hippocampus Middle	brain
7	chr16:71251800-71252800	Weak transcription	Fetal Stomach	stomach
8	chr16:71252000-71252600	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr16:71252000-71252600	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr16:71252200-71252600	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr16:71252400-71253200	Weak transcription	Brain Germinal Matrix	brain
12	chr16:71252400-71253200	Enhancers	Fetal Kidney	kidney
13	chr16:71252400-71254000	Enhancers	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links