Variant report

Variant	rs12302906
Chromosome Location	chr12:117474662-117474663
allele	A/G
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	chr12:117473852..117475862-chr12:117477409..117479027,2	K562	blood:
4	chr12:117474107..117476260-chr12:117479053..117480965,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10507278	1.00[JPT][hapmap]
rs10774891	0.85[CEU][hapmap]
rs10774896	0.92[TSI][hapmap]
rs10850741	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11838192	0.89[ASN][1000 genomes]
rs12299065	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16947275	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2173653	1.00[JPT][hapmap]
rs2270794	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3782193	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4130296	0.92[TSI][hapmap]
rs4238051	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs4522274	0.85[CEU][hapmap]
rs4562925	0.92[TSI][hapmap]
rs4767473	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs4767490	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59348125	0.94[ASN][1000 genomes]
rs60940473	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6490101	1.00[JPT][hapmap]
rs7131746	0.92[TSI][hapmap]
rs7302025	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7307907	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7311972	0.92[TSI][hapmap]
rs73405256	0.89[ASN][1000 genomes]
rs7954600	0.94[ASN][1000 genomes]
rs7957907	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7960610	1.00[JPT][hapmap]
rs7962339	0.94[ASN][1000 genomes]
rs7973925	0.94[ASN][1000 genomes]
rs7978725	0.84[ASN][1000 genomes]
rs7979277	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9308	0.94[ASN][1000 genomes]
rs9804817	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12302906	FBXW8	cis	Skin Sun Exposed Lower leg	GTEx
rs12302906	HRK	cis	multi-tissue	Pritchard
rs12302906	TESC	cis	parietal	SCAN
rs12302906	FBXW8	cis	lymphoblastoid	seeQTL

Chromatin state (count:49 , 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	chr12:117466400-117475600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:117466600-117479800	Weak transcription	Hela-S3	cervix
5	chr12:117467000-117475400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr12:117467000-117479600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:117467200-117475400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr12:117467400-117486000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr12:117468200-117477000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr12:117468600-117477400	Weak transcription	Primary B cells from cord blood	blood
11	chr12:117469200-117474800	Weak transcription	Lung	lung
12	chr12:117470400-117476800	Enhancers	Stomach Mucosa	stomach
13	chr12:117470800-117474800	Enhancers	Left Ventricle	heart
14	chr12:117470800-117476400	Strong transcription	Dnd41	blood
15	chr12:117470800-117483400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr12:117471200-117482800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr12:117471400-117479800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:117471600-117475200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:117471600-117480200	Weak transcription	Esophagus	oesophagus
20	chr12:117471600-117482600	Weak transcription	Primary B cells from peripheral blood	blood
21	chr12:117471800-117477200	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr12:117471800-117477400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr12:117472000-117475400	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr12:117472000-117482600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:117472200-117477200	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr12:117472200-117477400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr12:117472200-117478400	Weak transcription	Primary T cells from cord blood	blood
28	chr12:117472200-117479800	Weak transcription	Right Atrium	heart
29	chr12:117472400-117475000	Weak transcription	A549	lung
30	chr12:117472600-117475800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr12:117472600-117480200	Weak transcription	Ovary	ovary
32	chr12:117472600-117483000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr12:117472800-117475600	Weak transcription	Right Ventricle	heart
34	chr12:117473000-117475600	Weak transcription	Gastric	stomach
35	chr12:117473000-117477600	Weak transcription	K562	blood
36	chr12:117473400-117478400	Weak transcription	Brain Germinal Matrix	brain
37	chr12:117473800-117477600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:117474000-117475000	Enhancers	H1 Cell Line	embryonic stem cell
39	chr12:117474000-117479800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr12:117474200-117474800	Weak transcription	Fetal Thymus	thymus
41	chr12:117474200-117476800	Weak transcription	HepG2	liver
42	chr12:117474400-117478400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr12:117474600-117474800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr12:117474600-117476000	Bivalent Enhancer	Fetal Stomach	stomach
45	chr12:117474600-117476000	Weak transcription	Pancreas	Pancrea
46	chr12:117474600-117476800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr12:117474600-117477600	Weak transcription	Fetal Brain Female	brain
48	chr12:117474600-117479600	Weak transcription	Fetal Heart	heart
49	chr12:117474600-117479600	Weak transcription	Spleen	Spleen

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