Variant report

Variant	rs12911499
Chromosome Location	chr15:33318725-33318726
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	chr15:33317383..33320256-chr15:33356914..33360831,5	MCF-7	breast:
2	chr15:33317164..33319982-chr15:33363430..33365963,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248905	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12899651	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12900388	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12900907	0.86[EUR][1000 genomes]
rs12909281	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12909898	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12912725	1.00[EUR][1000 genomes]
rs12914708	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34039892	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34053978	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34184682	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34292665	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34508278	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs345799	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs34718785	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34747062	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35158642	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36094033	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs68165423	1.00[EUR][1000 genomes]
rs71462838	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71462839	1.00[EUR][1000 genomes]
rs71462840	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71462842	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71462843	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71462844	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71462845	0.95[EUR][1000 genomes]
rs71462846	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8042105	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456785	chr15:32926076-33352989	Genic enhancers Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv568913	chr15:32926076-33352989	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv903979	chr15:33144202-33550256	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1041609	chr15:33148035-33355999	Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv542339	chr15:33148035-33355999	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv1052966	chr15:33149753-33541951	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv542340	chr15:33149753-33541951	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv903981	chr15:33207082-33550256	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv568918	chr15:33244672-33446971	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv903982	chr15:33282844-33616150	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33306800-33321000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr15:33314800-33319000	Weak transcription	Fetal Kidney	kidney
3	chr15:33315000-33320400	Weak transcription	Duodenum Mucosa	Duodenum
4	chr15:33315200-33318800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr15:33315200-33318800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr15:33315200-33319600	Weak transcription	Adipose Nuclei	Adipose
7	chr15:33315200-33320000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr15:33315200-33321800	Weak transcription	Colonic Mucosa	Colon
9	chr15:33315200-33323400	Weak transcription	Esophagus	oesophagus
10	chr15:33315200-33323400	Weak transcription	NH-A	brain
11	chr15:33315200-33329400	Weak transcription	Pancreas	Pancrea
12	chr15:33315400-33318800	Weak transcription	Fetal Muscle Leg	muscle
13	chr15:33315400-33335400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr15:33315600-33318800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr15:33315600-33319600	Weak transcription	NHEK	skin
16	chr15:33315600-33323600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr15:33315800-33320000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr15:33315800-33323200	Weak transcription	HMEC	breast
19	chr15:33316000-33320000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr15:33316800-33322600	Enhancers	NHLF	lung
21	chr15:33317200-33323400	Enhancers	Muscle Satellite Cultured Cells	--
22	chr15:33317200-33324600	Enhancers	NHDF-Ad	bronchial
23	chr15:33317400-33319400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:33317400-33320000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr15:33317400-33323400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:33317600-33319200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:33317600-33322400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr15:33317800-33320200	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr15:33318000-33319200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr15:33318000-33319200	Enhancers	Thymus	Thymus
31	chr15:33318000-33320200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr15:33318200-33319200	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr15:33318200-33320200	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr15:33318200-33320400	Enhancers	Osteobl	bone
35	chr15:33318200-33322000	Enhancers	Stomach Mucosa	stomach
36	chr15:33318200-33322000	Enhancers	HSMM	muscle
37	chr15:33318200-33322200	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr15:33318200-33322800	Enhancers	Fetal Thymus	thymus
39	chr15:33318200-33323400	Enhancers	HSMMtube	muscle
40	chr15:33318400-33318800	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links