Variant report

Variant	rs11852998
Chromosome Location	chr15:33358639-33358640
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:33314218..33314802-chr15:33358026..33358783,2	MCF-7	breast:
2	chr15:33312296..33313936-chr15:33357129..33359638,2	MCF-7	breast:
3	chr15:33297830..33309224-chr15:33355310..33362883,25	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259686	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11072131	0.83[YRI][hapmap]
rs16964739	1.00[EUR][1000 genomes]
rs16964741	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16964825	1.00[EUR][1000 genomes]
rs16964922	1.00[EUR][1000 genomes]
rs28417580	1.00[EUR][1000 genomes]
rs28505971	1.00[EUR][1000 genomes]
rs28708877	1.00[EUR][1000 genomes]
rs7171336	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7172970	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7179866	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs73370897	1.00[EUR][1000 genomes]
rs9783740	1.00[TSI][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	nsv524708	chr15:33357262-33365334	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33348200-33360000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr15:33350400-33358800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:33350400-33358800	Weak transcription	Pancreas	Pancrea
4	chr15:33355400-33360600	Weak transcription	Right Ventricle	heart
5	chr15:33355600-33358800	Weak transcription	Small Intestine	intestine
6	chr15:33355600-33358800	Active TSS	Thymus	Thymus
7	chr15:33356400-33359200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:33356600-33359000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr15:33356600-33359800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr15:33356800-33361000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr15:33357000-33359200	Enhancers	Duodenum Mucosa	Duodenum
12	chr15:33357200-33358800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:33357200-33359200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr15:33357200-33359800	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr15:33357400-33358800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr15:33357400-33358800	Weak transcription	Esophagus	oesophagus
17	chr15:33357400-33358800	Weak transcription	HMEC	breast
18	chr15:33357400-33359400	Weak transcription	Fetal Kidney	kidney
19	chr15:33357400-33359600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr15:33357400-33359600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr15:33357400-33360200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr15:33357600-33359400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:33357800-33358800	Active TSS	NH-A	brain
24	chr15:33357800-33359200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr15:33358000-33358800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr15:33358000-33358800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr15:33358000-33360600	Active TSS	Colonic Mucosa	Colon
28	chr15:33358200-33358800	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr15:33358200-33359400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr15:33358200-33359600	Enhancers	HepG2	liver
31	chr15:33358200-33359800	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr15:33358200-33359800	Enhancers	Placenta	Placenta
33	chr15:33358200-33360400	Active TSS	Rectal Smooth Muscle	rectum
34	chr15:33358200-33360600	Active TSS	Stomach Mucosa	stomach
35	chr15:33358200-33361000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr15:33358400-33358800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr15:33358400-33358800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
38	chr15:33358400-33358800	Weak transcription	NHLF	lung
39	chr15:33358400-33359400	Enhancers	Fetal Thymus	thymus
40	chr15:33358400-33359600	Enhancers	Hela-S3	cervix
41	chr15:33358400-33359600	Enhancers	NHDF-Ad	bronchial
42	chr15:33358400-33360000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr15:33358400-33360000	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr15:33358400-33361800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:33358600-33358800	Active TSS	Osteobl	bone
46	chr15:33358600-33359000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
47	chr15:33358600-33359000	Active TSS	HSMMtube	muscle
48	chr15:33358600-33359200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr15:33358600-33359200	Active TSS	Lung	lung
50	chr15:33358600-33359200	Enhancers	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links