Variant report

Variant	rs12593870
Chromosome Location	chr15:75666650-75666651
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	chr15:75666202..75668425-chr15:75668606..75670439,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169375	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12591076	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12591309	0.93[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12591954	1.00[EUR][1000 genomes]
rs12592026	1.00[EUR][1000 genomes]
rs12592505	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12593372	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12594013	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs12594671	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28372857	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34234047	0.87[ASN][1000 genomes]
rs3803466	0.84[CHB][hapmap]
rs4886434	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4886435	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886445	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4886685	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4886686	0.84[ASN][1000 genomes]
rs4886689	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886697	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886701	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8032031	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8035510	1.00[EUR][1000 genomes]
rs8035796	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9788768	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039713	chr15:75394213-75674389	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv482859	chr15:75493899-75688451	Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	nsv1035829	chr15:75504534-75692417	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv531901	chr15:75600108-76019966	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
5	esv3445070	chr15:75623136-76045948	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
6	nsv530345	chr15:75628556-75951011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
7	nsv1048028	chr15:75637515-76019967	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
8	nsv542436	chr15:75637515-76019967	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
9	nsv904386	chr15:75655819-75673209	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75661600-75682200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:75662000-75666800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr15:75662200-75666800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:75662200-75667000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr15:75662200-75677600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr15:75662200-75699200	Strong transcription	Fetal Stomach	stomach
7	chr15:75662200-75715600	Strong transcription	Placenta	Placenta
8	chr15:75662400-75670400	Strong transcription	Fetal Muscle Leg	muscle
9	chr15:75662400-75678800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr15:75662400-75707600	Strong transcription	Primary T helper cells PMA-I stimulated	--
11	chr15:75662400-75717000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr15:75662400-75731400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:75662600-75670600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:75662600-75671800	Weak transcription	Stomach Mucosa	stomach
15	chr15:75662600-75678600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr15:75662600-75695000	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr15:75662600-75707400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr15:75662600-75708000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr15:75662600-75708000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr15:75662600-75708600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr15:75662600-75722800	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr15:75662800-75668200	Strong transcription	Fetal Lung	lung
23	chr15:75662800-75670600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr15:75662800-75682000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr15:75662800-75709400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr15:75662800-75723000	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr15:75663000-75670600	Strong transcription	Fetal Muscle Trunk	muscle
28	chr15:75663000-75672400	Strong transcription	Primary B cells from peripheral blood	blood
29	chr15:75663000-75673000	Strong transcription	Fetal Intestine Large	intestine
30	chr15:75663000-75690400	Strong transcription	Hela-S3	cervix
31	chr15:75663000-75695200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr15:75663000-75707800	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr15:75663000-75708000	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr15:75663000-75708200	Strong transcription	Fetal Thymus	thymus
35	chr15:75663000-75708600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr15:75663000-75709400	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr15:75663000-75710000	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr15:75663200-75667600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr15:75663200-75668400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr15:75663200-75668600	Strong transcription	Fetal Brain Female	brain
41	chr15:75663200-75670400	Strong transcription	Osteobl	bone
42	chr15:75663200-75673000	Strong transcription	GM12878-XiMat	blood
43	chr15:75663200-75674400	Strong transcription	A549	lung
44	chr15:75663200-75683200	Strong transcription	Adipose Nuclei	Adipose
45	chr15:75663200-75689000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:75663200-75699600	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr15:75663200-75706600	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr15:75663200-75707800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr15:75663200-75707800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr15:75663400-75668200	Strong transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links