Variant report

Variant	rs7962339
Chromosome Location	chr12:117471023-117471024
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:117470652..117475607-chr12:117477009..117480553,6	K562	blood:
2	chr12:117470409..117472666-chr12:117473842..117475716,2	MCF-7	breast:
3	chr12:117465370..117468011-chr12:117469598..117472527,2	K562	blood:
4	chr12:117461681..117464080-chr12:117470751..117473024,2	MCF-7	breast:
5	chr12:117469991..117472353-chr12:117476644..117478230,2	MCF-7	breast:
6	chr12:117469818..117471937-chr12:117535660..117537284,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000088992	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10507277	0.92[EUR][1000 genomes]
rs10507278	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10735099	0.83[EUR][1000 genomes]
rs10735102	0.85[EUR][1000 genomes]
rs10735103	0.89[EUR][1000 genomes]
rs10744886	0.87[EUR][1000 genomes]
rs10850733	0.85[ASN][1000 genomes]
rs10850741	0.94[ASN][1000 genomes]
rs10850743	0.92[EUR][1000 genomes]
rs11068264	0.85[EUR][1000 genomes]
rs11068277	0.85[EUR][1000 genomes]
rs11068296	0.94[EUR][1000 genomes]
rs11838192	0.94[ASN][1000 genomes]
rs12299065	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12302906	0.94[ASN][1000 genomes]
rs16947275	0.94[ASN][1000 genomes]
rs2173653	0.83[ASN][1000 genomes]
rs2242469	0.94[EUR][1000 genomes]
rs2270794	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2393111	0.85[EUR][1000 genomes]
rs3782193	0.83[ASN][1000 genomes]
rs4076700	0.85[EUR][1000 genomes]
rs4077519	0.86[EUR][1000 genomes]
rs4238051	0.85[ASN][1000 genomes]
rs4542506	0.89[EUR][1000 genomes]
rs4562926	0.80[EUR][1000 genomes]
rs4766812	0.84[EUR][1000 genomes]
rs4766814	0.84[EUR][1000 genomes]
rs4766815	0.85[EUR][1000 genomes]
rs4766821	0.90[EUR][1000 genomes]
rs4766822	0.85[EUR][1000 genomes]
rs4767473	0.85[ASN][1000 genomes]
rs4767474	0.85[EUR][1000 genomes]
rs4767478	0.87[EUR][1000 genomes]
rs4767480	0.87[EUR][1000 genomes]
rs4767483	0.87[EUR][1000 genomes]
rs4767484	0.90[EUR][1000 genomes]
rs4767485	0.89[EUR][1000 genomes]
rs4767487	0.90[EUR][1000 genomes]
rs4767488	0.86[EUR][1000 genomes]
rs4767489	0.90[EUR][1000 genomes]
rs4767490	0.94[ASN][1000 genomes]
rs4767491	0.90[EUR][1000 genomes]
rs4767493	0.91[EUR][1000 genomes]
rs59348125	1.00[ASN][1000 genomes]
rs60940473	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7137006	0.88[EUR][1000 genomes]
rs7137752	0.90[EUR][1000 genomes]
rs7297155	0.90[EUR][1000 genomes]
rs7297848	0.87[EUR][1000 genomes]
rs7302025	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7303882	0.87[EUR][1000 genomes]
rs7305948	0.83[ASN][1000 genomes]
rs7307907	0.85[ASN][1000 genomes]
rs7308498	0.90[EUR][1000 genomes]
rs7308734	0.87[EUR][1000 genomes]
rs7316144	0.90[EUR][1000 genomes]
rs73403241	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73405256	0.94[ASN][1000 genomes]
rs73405273	0.83[ASN][1000 genomes]
rs7954600	1.00[ASN][1000 genomes]
rs7957907	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7958030	0.89[EUR][1000 genomes]
rs7959666	0.92[EUR][1000 genomes]
rs7973240	0.86[EUR][1000 genomes]
rs7973925	1.00[ASN][1000 genomes]
rs7977598	0.91[EUR][1000 genomes]
rs7978725	0.89[ASN][1000 genomes]
rs7979277	1.00[ASN][1000 genomes]
rs9308	1.00[ASN][1000 genomes]
rs9804817	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]

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	nsv832524	chr12:117314110-117496576	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv519118	chr12:117386085-117521180	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv899541	chr12:117414974-117497066	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7962339	FBXW8	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117452800-117479000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr12:117462000-117477400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr12:117464000-117471800	Weak transcription	K562	blood
4	chr12:117466200-117474600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:117466400-117473800	Weak transcription	Aorta	Aorta
6	chr12:117466400-117475600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:117466600-117479800	Weak transcription	Hela-S3	cervix
8	chr12:117467000-117475400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr12:117467000-117479600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:117467200-117475400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr12:117467400-117486000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr12:117468200-117471600	Weak transcription	HSMMtube	muscle
13	chr12:117468200-117477000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr12:117468600-117471600	Weak transcription	HepG2	liver
15	chr12:117468600-117477400	Weak transcription	Primary B cells from cord blood	blood
16	chr12:117469000-117471600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:117469200-117471200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr12:117469200-117474800	Weak transcription	Lung	lung
19	chr12:117469600-117471600	Enhancers	Primary B cells from peripheral blood	blood
20	chr12:117469800-117474600	Enhancers	Fetal Heart	heart
21	chr12:117470000-117472000	Enhancers	Pancreas	Pancrea
22	chr12:117470000-117472200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:117470200-117471200	Bivalent Enhancer	GM12878-XiMat	blood
24	chr12:117470200-117472200	Bivalent Enhancer	Fetal Thymus	thymus
25	chr12:117470200-117472600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr12:117470400-117471200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr12:117470400-117471200	Flanking Active TSS	Brain Hippocampus Middle	brain
28	chr12:117470400-117471200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr12:117470400-117471600	Bivalent Enhancer	Placenta	Placenta
30	chr12:117470400-117471800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr12:117470400-117471800	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr12:117470400-117472000	Enhancers	H1 Cell Line	embryonic stem cell
33	chr12:117470400-117472400	Strong transcription	A549	lung
34	chr12:117470400-117476800	Enhancers	Stomach Mucosa	stomach
35	chr12:117470600-117471200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
36	chr12:117470600-117471200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr12:117470600-117471200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr12:117470600-117471200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:117470600-117471200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
40	chr12:117470600-117471400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr12:117470600-117471400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:117470600-117471400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
43	chr12:117470600-117471400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
44	chr12:117470600-117471600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr12:117470600-117471600	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr12:117470600-117471600	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr12:117470600-117471600	Enhancers	Psoas Muscle	Psoas
48	chr12:117470600-117471800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
49	chr12:117470600-117471800	Enhancers	Spleen	Spleen
50	chr12:117470600-117472200	Enhancers	Brain Angular Gyrus	brain

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