Variant report

Variant	rs13095806
Chromosome Location	chr3:156456060-156456061
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	chr3:156449917..156452057-chr3:156455354..156457337,2	MCF-7	breast:
2	chr3:156455142..156458106-chr3:156458193..156461275,4	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11709829	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11917436	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12485328	0.85[YRI][hapmap]
rs12638253	0.80[JPT][hapmap]
rs12696042	0.82[YRI][hapmap]
rs13061457	0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs13068223	0.96[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13322318	0.83[JPT][hapmap]
rs13322900	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1469536	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1560414	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2171542	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2321290	0.80[JPT][hapmap]
rs2321292	0.80[JPT][hapmap]
rs237250	0.83[TSI][hapmap]
rs34111024	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs344027	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs344035	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs345985	0.94[CHB][hapmap]
rs36126086	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3851992	0.94[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap]
rs4098	0.84[GIH][hapmap]
rs4680312	0.80[JPT][hapmap]
rs6766154	0.81[YRI][hapmap]
rs7617108	0.85[YRI][hapmap]
rs7637701	0.80[JPT][hapmap]
rs7638625	0.80[JPT][hapmap]
rs8792	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9837038	0.80[JPT][hapmap]
rs9838430	0.88[YRI][hapmap]
rs9847187	0.80[JPT][hapmap]
rs985855	0.82[YRI][hapmap]
rs9865905	0.80[JPT][hapmap]
rs9868587	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871817	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156445600-156459600	Weak transcription	Brain Substantia Nigra	brain
2	chr3:156446400-156464600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:156446400-156467000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:156447800-156457400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:156447800-156457400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:156447800-156464200	Weak transcription	HSMM	muscle
7	chr3:156447800-156464600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:156447800-156465000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr3:156447800-156467000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:156448200-156462800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:156448200-156464200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:156448400-156464600	Weak transcription	NHEK	skin
13	chr3:156450400-156459200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:156450800-156458600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:156450800-156461600	Weak transcription	HepG2	liver
16	chr3:156454200-156457000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:156455400-156457400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:156455600-156456400	Enhancers	Fetal Intestine Large	intestine
19	chr3:156455600-156456600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:156456000-156461800	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links