Variant report

Variant	rs11960506
Chromosome Location	chr5:95964055-95964056
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:95962754..95968222-chr5:95995730..96000718,6	MCF-7	breast:
2	chr5:95957625..95959898-chr5:95962941..95964481,2	MCF-7	breast:
3	chr5:95962343..95964474-chr5:95964579..95968462,3	K562	blood:

Variant related genes	Relation type
ENSG00000153113	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10036002	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10476555	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11958228	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13354939	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13358372	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17086432	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17086439	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17086458	0.90[CHB][hapmap]
rs28708687	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4254932	1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];0.83[ASN][1000 genomes]
rs4869300	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4869301	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4869302	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6880029	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6880040	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs73134563	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs73134569	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs73136632	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030444	chr5:95353620-95995619	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv537810	chr5:95353620-95995619	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1024964	chr5:95742124-96065492	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv537811	chr5:95742124-96065492	Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95951400-95965000	Weak transcription	HUVEC	blood vessel
2	chr5:95952200-95964600	Weak transcription	Esophagus	oesophagus
3	chr5:95954000-95965400	Weak transcription	Aorta	Aorta
4	chr5:95958400-95965400	Weak transcription	NHLF	lung
5	chr5:95961200-95964200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:95961200-95966200	Enhancers	HSMM	muscle
7	chr5:95961200-95966200	Enhancers	NH-A	brain
8	chr5:95961200-95966400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr5:95961200-95966600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr5:95961200-95967200	Enhancers	HMEC	breast
11	chr5:95961400-95964600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:95961400-95967000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:95962000-95966200	Enhancers	HSMMtube	muscle
14	chr5:95962000-95966400	Enhancers	Osteobl	bone
15	chr5:95962200-95964400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:95962200-95967000	Enhancers	Muscle Satellite Cultured Cells	--
17	chr5:95962400-95965600	Weak transcription	Right Atrium	heart
18	chr5:95962600-95965000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:95963000-95964200	Weak transcription	Fetal Lung	lung
20	chr5:95963000-95964400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr5:95963200-95964600	Enhancers	NHDF-Ad	bronchial
22	chr5:95963400-95964400	Enhancers	Fetal Intestine Small	intestine
23	chr5:95963400-95965000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:95963400-95966400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:95963400-95966800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr5:95963400-95967000	Enhancers	Hela-S3	cervix
27	chr5:95963600-95964200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr5:95963600-95964200	Weak transcription	Stomach Mucosa	stomach
29	chr5:95963800-95964200	Enhancers	Liver	Liver
30	chr5:95963800-95964200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr5:95963800-95964600	Enhancers	HepG2	liver
32	chr5:95963800-95964800	Flanking Active TSS	A549	lung
33	chr5:95963800-95965000	Enhancers	NHEK	skin
34	chr5:95963800-95965200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links