Variant report

Variant	rs11917436
Chromosome Location	chr3:156465628-156465629
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	chr3:156462787..156465779-chr3:156495644..156498107,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SSR3-3	chr3:156465135-156468203	ENSG00000240875
2	lnc-SSR3-3	chr3:156464967-156468203	NONHSAT092863
3	lnc-RP11-6F2.7.1-5	chr3:156465140-156465681	NONHSAT092864
4	lnc-SSR3-3	chr3:156465132-156468203	NR_038387

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11709829	0.90[ASN][1000 genomes]
rs13061457	0.82[ASN][1000 genomes]
rs13068223	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13095806	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13322900	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1469536	0.89[ASN][1000 genomes]
rs1560414	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs168247	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2171542	0.81[ASN][1000 genomes]
rs237250	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34111024	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs343999	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs344003	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs344028	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs344034	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs344035	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs344067	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs36126086	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs374341	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868587	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]

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:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156446400-156467000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:156447800-156467000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:156460000-156468400	Weak transcription	Pancreas	Pancrea
4	chr3:156462000-156466600	Weak transcription	Right Atrium	heart
5	chr3:156462200-156467000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:156464200-156465800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:156464400-156466400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:156464600-156468000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:156464800-156466800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:156464800-156467200	Weak transcription	Osteobl	bone
11	chr3:156465000-156465800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:156465000-156466400	ZNF genes & repeats	HMEC	breast
13	chr3:156465400-156465800	ZNF genes & repeats	HSMM	muscle
14	chr3:156465400-156466000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:156465400-156467200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:156465600-156466000	Weak transcription	NHEK	skin
17	chr3:156465600-156466200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr3:156465600-156466200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:156465600-156466400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:156465600-156466600	Weak transcription	A549	lung
21	chr3:156465600-156467200	Weak transcription	NHDF-Ad	bronchial
22	chr3:156465600-156467600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links