Variant report

Variant	rs12665780
Chromosome Location	chr6:25365744-25365745
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25360833..25363264-chr6:25364832..25366836,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs28713764	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28744391	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55691071	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55708418	1.00[ASN][1000 genomes]
rs55935768	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56004173	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56084108	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56146948	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6906404	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6906654	1.00[JPT][hapmap]
rs6929831	1.00[CEU][hapmap]
rs73383409	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73383427	1.00[ASN][1000 genomes]
rs9356968	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv601168	chr6:25346334-25393306	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25359600-25366000	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr6:25359800-25367200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:25360000-25367200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:25360000-25367400	Weak transcription	Lung	lung
5	chr6:25360000-25367400	Weak transcription	Right Atrium	heart
6	chr6:25360400-25366000	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr6:25360400-25366400	Weak transcription	Gastric	stomach
8	chr6:25360400-25367600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:25360400-25367600	Weak transcription	Pancreas	Pancrea
10	chr6:25360400-25367800	Weak transcription	Brain Germinal Matrix	brain
11	chr6:25360400-25369200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:25360800-25367200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr6:25360800-25367600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:25360800-25369800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr6:25361000-25367000	Weak transcription	Fetal Intestine Small	intestine
16	chr6:25361000-25367200	Weak transcription	Fetal Intestine Large	intestine
17	chr6:25361000-25367200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr6:25361000-25367400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:25361000-25369200	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr6:25361000-25369400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr6:25361000-25369400	Weak transcription	Left Ventricle	heart
22	chr6:25361000-25369800	Weak transcription	Brain Substantia Nigra	brain
23	chr6:25361200-25366400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:25361200-25366600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr6:25361200-25367200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr6:25362000-25367000	Weak transcription	NHLF	lung
27	chr6:25362000-25367200	Weak transcription	Brain Anterior Caudate	brain
28	chr6:25362600-25367200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr6:25362800-25366400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:25362800-25367600	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr6:25363000-25366000	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr6:25363000-25366400	Weak transcription	NHEK	skin
33	chr6:25363200-25365800	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr6:25363400-25367200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr6:25363600-25366200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:25363800-25366200	Weak transcription	HMEC	breast
37	chr6:25363800-25366600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr6:25363800-25367000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr6:25363800-25367400	Weak transcription	Fetal Lung	lung
40	chr6:25364000-25367200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:25364000-25367200	Weak transcription	Primary B cells from peripheral blood	blood
42	chr6:25364000-25367200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:25364200-25367200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:25364400-25366400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr6:25364400-25367000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr6:25364400-25367000	Weak transcription	Adipose Nuclei	Adipose
47	chr6:25364400-25367200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:25364600-25366600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:25364800-25367000	Enhancers	Fetal Thymus	thymus
50	chr6:25365200-25366600	Enhancers	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links