Variant report

Variant	rs13177252
Chromosome Location	chr5:80308561-80308562
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:80304567..80306339-chr5:80307173..80308776,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12152989	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12153055	0.81[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13156982	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13157328	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13176380	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13179550	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13182907	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13183094	0.86[YRI][hapmap]
rs13183890	0.81[YRI][hapmap]
rs17409544	1.00[JPT][hapmap]
rs4704694	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4704695	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6879497	0.83[CEU][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs73766165	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv598747	chr5:79996632-80322712	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1021784	chr5:80023679-80313586	ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv537787	chr5:80023679-80313586	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv830358	chr5:80197105-80358920	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv830360	chr5:80283278-80446040	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv4897	chr5:80284196-80330223	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80300000-80313000	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr5:80300400-80312800	Weak transcription	Brain Hippocampus Middle	brain
3	chr5:80300400-80316600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:80300400-80318400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr5:80303000-80311600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:80303000-80312800	Weak transcription	Brain Angular Gyrus	brain
7	chr5:80303000-80318200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:80303800-80314400	Weak transcription	HepG2	liver
9	chr5:80304400-80309400	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr5:80305000-80310200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr5:80305000-80311200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr5:80305000-80315000	Weak transcription	Left Ventricle	heart
13	chr5:80305200-80309400	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr5:80305200-80318200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr5:80305400-80310200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr5:80305800-80312800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr5:80306000-80310200	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr5:80307200-80310000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr5:80307200-80310000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr5:80307200-80311800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr5:80307400-80312800	Weak transcription	Fetal Lung	lung
22	chr5:80308000-80309000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr5:80308200-80308600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr5:80308200-80308800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr5:80308400-80309200	Strong transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links