Variant report

Variant	rs12280959
Chromosome Location	chr11:18595915-18595916
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:18594808..18597931-chr11:18609017..18611085,3	MCF-7	breast:
2	chr11:18595002..18597166-chr11:18603669..18605204,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151116	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11024722	0.81[AFR][1000 genomes]
rs12289644	0.83[AFR][1000 genomes]
rs12577132	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12577416	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12577619	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2291753	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34150212	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7109496	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv1042155	chr11:18435855-18697576	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv1046886	chr11:18547568-18781448	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv540956	chr11:18547568-18781448	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
6	esv3442757	chr11:18595343-18596606	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18549600-18608600	Weak transcription	Fetal Heart	heart
2	chr11:18549600-18609000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr11:18549600-18609000	Weak transcription	Fetal Brain Male	brain
4	chr11:18549800-18600600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr11:18552600-18601400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr11:18562200-18598200	Weak transcription	Stomach Mucosa	stomach
7	chr11:18563200-18601200	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr11:18563800-18608800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr11:18565200-18609400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:18566200-18601000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr11:18567400-18601000	Strong transcription	Placenta	Placenta
12	chr11:18568600-18600800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr11:18571800-18601200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr11:18574400-18609400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:18575000-18609200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr11:18575200-18609200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr11:18576600-18596400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr11:18576800-18599200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr11:18577400-18599200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr11:18578000-18600600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr11:18578000-18608800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr11:18578000-18609000	Weak transcription	Right Ventricle	heart
23	chr11:18578200-18609000	Weak transcription	Primary T cells from cord blood	blood
24	chr11:18578400-18609000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr11:18578600-18608400	Weak transcription	Psoas Muscle	Psoas
26	chr11:18579600-18600800	Weak transcription	Colonic Mucosa	Colon
27	chr11:18580000-18596400	Weak transcription	HepG2	liver
28	chr11:18580000-18608600	Weak transcription	Hela-S3	cervix
29	chr11:18580200-18608600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr11:18581000-18609000	Weak transcription	Pancreas	Pancrea
31	chr11:18582600-18600600	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr11:18583000-18608200	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr11:18583000-18609400	Weak transcription	Esophagus	oesophagus
34	chr11:18583200-18597000	Weak transcription	Brain Substantia Nigra	brain
35	chr11:18583200-18604600	Weak transcription	Gastric	stomach
36	chr11:18584200-18600200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr11:18584200-18608000	Weak transcription	Small Intestine	intestine
38	chr11:18584400-18609800	Weak transcription	Spleen	Spleen
39	chr11:18585000-18597400	Weak transcription	Thymus	Thymus
40	chr11:18585800-18608600	Weak transcription	Fetal Brain Female	brain
41	chr11:18586200-18596000	Weak transcription	Colon Smooth Muscle	Colon
42	chr11:18586400-18596000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr11:18586400-18609000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr11:18587200-18598800	Weak transcription	GM12878-XiMat	blood
45	chr11:18587800-18598200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr11:18588200-18608800	Weak transcription	Fetal Kidney	kidney
47	chr11:18590000-18600000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr11:18590200-18601200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr11:18590800-18601200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr11:18590800-18601400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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