Variant report

Variant	rs9308
Chromosome Location	chr12:117476896-117476897
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:117469991..117472353-chr12:117476644..117478230,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10774896	0.82[EUR][1000 genomes]
rs10850733	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10850741	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11838192	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12299065	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12302906	0.94[ASN][1000 genomes]
rs16947275	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2173653	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2270794	0.81[GIH][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3782193	0.90[GIH][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4074147	0.82[EUR][1000 genomes]
rs4238051	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4766818	0.82[EUR][1000 genomes]
rs4766820	0.82[EUR][1000 genomes]
rs4767473	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4767482	0.82[EUR][1000 genomes]
rs4767490	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59348125	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60940473	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6490102	0.82[EUR][1000 genomes]
rs7131746	0.81[EUR][1000 genomes]
rs7302025	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7303752	0.83[EUR][1000 genomes]
rs7305948	0.83[ASN][1000 genomes]
rs7307907	0.85[ASN][1000 genomes]
rs7311972	0.82[EUR][1000 genomes]
rs73405256	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73405273	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7954600	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7954824	0.82[EUR][1000 genomes]
rs7957907	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7962339	1.00[ASN][1000 genomes]
rs7973925	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978725	0.98[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7979277	1.00[ASW][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.96[MKK][hapmap];0.84[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9804817	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	esv1804583	chr12:117472107-117525169	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9308	FBXW8	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:48 , 50 per page) page: 1

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	chr12:117466600-117479800	Weak transcription	Hela-S3	cervix
4	chr12:117467000-117479600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:117467400-117486000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr12:117468200-117477000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr12:117468600-117477400	Weak transcription	Primary B cells from cord blood	blood
8	chr12:117470800-117483400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:117471200-117482800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr12:117471400-117479800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:117471600-117480200	Weak transcription	Esophagus	oesophagus
12	chr12:117471600-117482600	Weak transcription	Primary B cells from peripheral blood	blood
13	chr12:117471800-117477200	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr12:117471800-117477400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr12:117472000-117482600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:117472200-117477200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr12:117472200-117477400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr12:117472200-117478400	Weak transcription	Primary T cells from cord blood	blood
19	chr12:117472200-117479800	Weak transcription	Right Atrium	heart
20	chr12:117472600-117480200	Weak transcription	Ovary	ovary
21	chr12:117472600-117483000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:117473000-117477600	Weak transcription	K562	blood
23	chr12:117473400-117478400	Weak transcription	Brain Germinal Matrix	brain
24	chr12:117473800-117477600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:117474000-117479800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr12:117474400-117478400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr12:117474600-117477600	Weak transcription	Fetal Brain Female	brain
28	chr12:117474600-117479600	Weak transcription	Fetal Heart	heart
29	chr12:117474600-117479600	Weak transcription	Spleen	Spleen
30	chr12:117474800-117479600	Weak transcription	Left Ventricle	heart
31	chr12:117475000-117477200	Strong transcription	A549	lung
32	chr12:117475600-117477000	Genic enhancers	Gastric	stomach
33	chr12:117476000-117477000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr12:117476000-117477000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr12:117476000-117478200	Strong transcription	Pancreas	Pancrea
36	chr12:117476000-117479600	Weak transcription	Fetal Intestine Large	intestine
37	chr12:117476000-117479600	Weak transcription	Fetal Intestine Small	intestine
38	chr12:117476200-117477000	Weak transcription	Fetal Stomach	stomach
39	chr12:117476200-117477600	Weak transcription	Brain Anterior Caudate	brain
40	chr12:117476200-117477600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr12:117476400-117477400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr12:117476400-117479800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr12:117476400-117484600	Weak transcription	Dnd41	blood
44	chr12:117476600-117477600	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr12:117476600-117479800	Weak transcription	Right Ventricle	heart
46	chr12:117476800-117477400	Weak transcription	Stomach Mucosa	stomach
47	chr12:117476800-117478000	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr12:117476800-117478200	Strong transcription	HepG2	liver

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