Variant report

Variant	rs11954162
Chromosome Location	chr5:120138772-120138773
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:119991478..119992421-chr5:120138412..120139232,3	MCF-7	breast:

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10038014	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10900741	0.88[ASN][1000 genomes]
rs10900742	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11241566	0.87[ASN][1000 genomes]
rs11241567	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11241568	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11739528	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11749110	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11749221	0.88[ASN][1000 genomes]
rs11953061	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11959710	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12521338	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1584469	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17444067	0.88[ASN][1000 genomes]
rs17502651	0.83[TSI][hapmap]
rs17503473	0.88[ASN][1000 genomes]
rs2084516	0.88[ASN][1000 genomes]
rs2406164	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4317354	0.80[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4340941	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4412134	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4576171	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4624817	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4631209	0.84[EUR][1000 genomes]
rs55833879	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56043914	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56366998	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56405820	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56412481	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58897895	0.84[ASN][1000 genomes]
rs61358955	0.86[ASN][1000 genomes]
rs62379821	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62379822	0.81[ASN][1000 genomes]
rs62379823	0.83[ASN][1000 genomes]
rs62379824	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62379825	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62379836	0.84[ASN][1000 genomes]
rs62379837	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62379838	0.88[ASN][1000 genomes]
rs62379839	0.88[ASN][1000 genomes]
rs62379840	0.88[ASN][1000 genomes]
rs62379841	0.88[ASN][1000 genomes]
rs62379842	0.88[ASN][1000 genomes]
rs62379846	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62379847	0.92[ASN][1000 genomes]
rs62379853	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62381082	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62381083	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62381087	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62381088	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62381109	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62381111	0.81[ASN][1000 genomes]
rs6595262	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66653209	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66694560	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6864919	0.81[ASN][1000 genomes]
rs6869346	0.80[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6879947	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6885643	0.81[ASN][1000 genomes]
rs6891234	0.91[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72781627	0.86[ASN][1000 genomes]
rs72783651	0.91[ASN][1000 genomes]
rs72783652	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72783657	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7701853	0.82[ASN][1000 genomes]
rs7704971	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7711644	0.82[ASN][1000 genomes]
rs7711647	0.82[ASN][1000 genomes]
rs7714971	0.80[TSI][hapmap]
rs7716293	0.82[ASN][1000 genomes]
rs7717354	0.82[ASN][1000 genomes]
rs7717562	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7721615	0.82[ASN][1000 genomes]
rs7725293	0.86[ASN][1000 genomes]
rs7729364	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7730641	0.91[ASN][1000 genomes]
rs7735871	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9327165	0.91[ASN][1000 genomes]
rs9686731	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9687387	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031453	chr5:119843593-120393038	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv599603	chr5:119953529-120317035	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv949415	chr5:119957645-120459183	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv830465	chr5:119973839-120151853	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1030613	chr5:119980213-120301205	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1029773	chr5:120018166-120213999	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1031403	chr5:120044993-120222128	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1033992	chr5:120045247-120232155	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1034523	chr5:120046649-120213999	Enhancers ZNF genes & repeats Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv537886	chr5:120046649-120213999	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1032430	chr5:120046652-120222128	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv599604	chr5:120046798-120223491	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv882788	chr5:120047147-120162357	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv1025535	chr5:120050070-120222128	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	esv3369974	chr5:120051746-120319085	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv882789	chr5:120056258-120190213	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv1017521	chr5:120061733-120175806	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv1026309	chr5:120063385-120147180	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	nsv1016322	chr5:120063385-120181846	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv882790	chr5:120066820-120162357	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	nsv830466	chr5:120086428-120259016	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
22	nsv599605	chr5:120096907-120151772	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	nsv882791	chr5:120100225-120293328	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
24	nsv1031293	chr5:120100625-120157821	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
25	nsv524748	chr5:120104848-120219340	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
26	nsv1032601	chr5:120138772-120163808	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:120137600-120139000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:120137800-120139000	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr5:120138000-120142000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr5:120138400-120138800	Enhancers	H9 Cell Line	embryonic stem cell
5	chr5:120138400-120138800	Enhancers	Muscle Satellite Cultured Cells	--
6	chr5:120138400-120139000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:120138400-120139000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:120138400-120139000	Active TSS	Brain Anterior Caudate	brain
9	chr5:120138400-120139000	Active TSS	Brain Hippocampus Middle	brain
10	chr5:120138400-120139000	Enhancers	HSMM	muscle
11	chr5:120138400-120139000	Flanking Active TSS	NHDF-Ad	bronchial
12	chr5:120138400-120139000	Enhancers	Osteobl	bone
13	chr5:120138600-120139000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links