Variant report

Variant	rs1947504
Chromosome Location	chr12:64361462-64361463
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:64361242..64364159-chr12:64364503..64367184,2	MCF-7	breast:
2	chr12:64360379..64362795-chr12:64366737..64368794,2	MCF-7	breast:
3	chr12:64238259..64239781-chr12:64360644..64362530,2	MCF-7	breast:
4	chr12:64348224..64350192-chr12:64359739..64362105,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196935	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11175217	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11175227	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs1350138	0.81[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap]
rs1350140	0.82[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.82[TSI][hapmap]
rs1962538	0.99[ASN][1000 genomes]
rs2054150	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3741607	0.81[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap]
rs4516056	0.94[JPT][hapmap]
rs4604983	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6581515	0.82[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs7300256	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7300468	0.82[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.82[MKK][hapmap]
rs7313754	0.82[CHB][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.82[MKK][hapmap]
rs7957913	0.82[CHB][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap]
rs9668855	0.81[CHB][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046836	chr12:63392391-64377169	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv832442	chr12:64228071-64442771	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv559201	chr12:64333212-64366408	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1947504	DPY19L2	cis	cerebellum	SCAN
rs1947504	C12orf66	cis	cerebellum	SCAN
rs1947504	MSRB3	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64312400-64385000	Weak transcription	Aorta	Aorta
2	chr12:64344600-64363800	Weak transcription	Fetal Intestine Small	intestine
3	chr12:64345400-64363800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:64346000-64365400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:64355200-64361600	Weak transcription	Fetal Brain Male	brain
6	chr12:64355400-64362200	Weak transcription	Pancreas	Pancrea
7	chr12:64355600-64363800	Weak transcription	Adipose Nuclei	Adipose
8	chr12:64357200-64362400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr12:64358400-64362400	Weak transcription	Psoas Muscle	Psoas
10	chr12:64358600-64363000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr12:64358800-64362200	Weak transcription	Brain Substantia Nigra	brain
12	chr12:64358800-64363200	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr12:64359400-64362200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:64359400-64362600	Enhancers	Osteobl	bone
15	chr12:64359600-64362800	Enhancers	NHDF-Ad	bronchial
16	chr12:64359800-64362800	Enhancers	Muscle Satellite Cultured Cells	--
17	chr12:64359800-64364000	Enhancers	NHLF	lung
18	chr12:64360000-64361600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr12:64360000-64361800	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr12:64360000-64362400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:64360200-64362000	Enhancers	NHEK	skin
22	chr12:64360400-64361600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:64360400-64361800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:64360400-64362000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr12:64360400-64362000	Enhancers	A549	lung
26	chr12:64360400-64362600	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr12:64360600-64363800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr12:64360600-64363800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:64360600-64365600	Weak transcription	Small Intestine	intestine
30	chr12:64360800-64361800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr12:64360800-64362200	Enhancers	HUVEC	blood vessel
32	chr12:64360800-64362800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:64360800-64363600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr12:64360800-64364200	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr12:64360800-64365000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr12:64361000-64361600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr12:64361000-64361800	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr12:64361000-64361800	Enhancers	HMEC	breast
39	chr12:64361000-64361800	Enhancers	NH-A	brain
40	chr12:64361000-64362600	Enhancers	HSMM	muscle
41	chr12:64361000-64362800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr12:64361000-64362800	Enhancers	Left Ventricle	heart
43	chr12:64361000-64363200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:64361000-64363200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:64361000-64364000	Enhancers	Fetal Brain Female	brain
46	chr12:64361200-64361800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:64361200-64362000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:64361200-64362200	Weak transcription	Right Atrium	heart
49	chr12:64361200-64362400	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr12:64361200-64362600	Weak transcription	H9 Cell Line	embryonic stem cell

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