Variant report

Variant	rs12911380
Chromosome Location	chr15:56200634-56200635
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	chr15:56199193..56201528-chr15:56218643..56221076,2	MCF-7	breast:
2	chr15:56199692..56201562-chr15:56202025..56204154,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10518823	0.83[AMR][1000 genomes]
rs12898478	0.83[AMR][1000 genomes]
rs12908286	0.83[AMR][1000 genomes]
rs12911101	0.83[AMR][1000 genomes]
rs17819270	0.83[AMR][1000 genomes]
rs1912397	0.83[AMR][1000 genomes]
rs1912403	0.83[AMR][1000 genomes]
rs34333169	0.83[AMR][1000 genomes]
rs34718758	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34727807	0.83[AMR][1000 genomes]
rs34995202	0.83[AMR][1000 genomes]
rs35313340	0.83[AMR][1000 genomes]
rs36110450	0.81[EUR][1000 genomes]
rs66857236	0.83[AMR][1000 genomes]
rs67046147	0.83[AMR][1000 genomes]
rs67825863	0.83[AMR][1000 genomes]
rs7172454	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv569542	chr15:56185262-56210929	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56176000-56216200	Weak transcription	Fetal Intestine Small	intestine
2	chr15:56188400-56207800	Weak transcription	Primary T cells from cord blood	blood
3	chr15:56188600-56218400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr15:56190000-56220000	Weak transcription	Pancreas	Pancrea
5	chr15:56190200-56201800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:56190200-56221200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr15:56190400-56219800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr15:56192400-56207800	Weak transcription	Liver	Liver
9	chr15:56192600-56200800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr15:56192600-56209000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr15:56199200-56203600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr15:56199400-56201000	Enhancers	HUVEC	blood vessel
13	chr15:56199400-56202600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr15:56199400-56203800	Flanking Active TSS	A549	lung
15	chr15:56199600-56200800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:56199600-56201600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr15:56199800-56201400	Active TSS	Psoas Muscle	Psoas
18	chr15:56199800-56203600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr15:56200000-56201400	Enhancers	HSMM	muscle
20	chr15:56200000-56201800	Enhancers	HMEC	breast
21	chr15:56200000-56202200	Enhancers	NH-A	brain
22	chr15:56200000-56202800	Enhancers	Osteobl	bone
23	chr15:56200000-56203200	Enhancers	HSMMtube	muscle
24	chr15:56200200-56201400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr15:56200200-56202200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr15:56200200-56202800	Enhancers	NHDF-Ad	bronchial
27	chr15:56200200-56203600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr15:56200200-56208600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr15:56200200-56213200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:56200400-56200800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr15:56200400-56202600	Enhancers	Hela-S3	cervix
32	chr15:56200400-56203600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr15:56200400-56209000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:56200600-56200800	Enhancers	Placenta Amnion	Placenta Amnion
35	chr15:56200600-56200800	Flanking Active TSS	NHEK	skin
36	chr15:56200600-56201400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr15:56200600-56202000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:56200600-56202200	Enhancers	NHLF	lung
39	chr15:56200600-56203200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links