Variant report

Variant	rs7978725
Chromosome Location	chr12:117477816-117477817
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:117473852..117475862-chr12:117477409..117479027,2	K562	blood:
2	chr12:117477087..117480724-chr12:117486826..117489814,3	MCF-7	breast:
3	chr12:117470652..117475607-chr12:117477009..117480553,6	K562	blood:
4	chr12:117477334..117479654-chr12:117535029..117537514,2	MCF-7	breast:
5	chr12:117469991..117472353-chr12:117476644..117478230,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000088992	Chromatin interaction
ENSG00000258285	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10850741	0.84[ASN][1000 genomes]
rs11838192	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12299065	0.84[ASN][1000 genomes]
rs12302906	0.84[ASN][1000 genomes]
rs16947275	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2270794	0.89[ASN][1000 genomes]
rs4767490	0.84[ASN][1000 genomes]
rs59348125	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs60940473	0.84[ASN][1000 genomes]
rs7302025	0.84[ASN][1000 genomes]
rs73405256	0.84[ASN][1000 genomes]
rs7954600	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7957907	0.84[ASN][1000 genomes]
rs7962339	0.89[ASN][1000 genomes]
rs7973925	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7979277	0.98[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7979546	0.89[EUR][1000 genomes]
rs9308	0.98[AFR][1000 genomes];0.89[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
rs7978725	FBXW8	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:50 , 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	chr12:117466600-117479800	Weak transcription	Hela-S3	cervix
3	chr12:117467000-117479600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:117467400-117486000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr12:117470800-117483400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr12:117471200-117482800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:117471400-117479800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:117471600-117480200	Weak transcription	Esophagus	oesophagus
9	chr12:117471600-117482600	Weak transcription	Primary B cells from peripheral blood	blood
10	chr12:117472000-117482600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:117472200-117478400	Weak transcription	Primary T cells from cord blood	blood
12	chr12:117472200-117479800	Weak transcription	Right Atrium	heart
13	chr12:117472600-117480200	Weak transcription	Ovary	ovary
14	chr12:117472600-117483000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr12:117473400-117478400	Weak transcription	Brain Germinal Matrix	brain
16	chr12:117474000-117479800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr12:117474400-117478400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr12:117474600-117479600	Weak transcription	Fetal Heart	heart
19	chr12:117474600-117479600	Weak transcription	Spleen	Spleen
20	chr12:117474800-117479600	Weak transcription	Left Ventricle	heart
21	chr12:117476000-117478200	Strong transcription	Pancreas	Pancrea
22	chr12:117476000-117479600	Weak transcription	Fetal Intestine Large	intestine
23	chr12:117476000-117479600	Weak transcription	Fetal Intestine Small	intestine
24	chr12:117476400-117479800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:117476400-117484600	Weak transcription	Dnd41	blood
26	chr12:117476600-117479800	Weak transcription	Right Ventricle	heart
27	chr12:117476800-117478000	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr12:117476800-117478200	Strong transcription	HepG2	liver
29	chr12:117477000-117478200	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr12:117477200-117479600	Weak transcription	A549	lung
31	chr12:117477400-117478200	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr12:117477400-117479200	Enhancers	Primary B cells from cord blood	blood
33	chr12:117477400-117481200	Enhancers	Primary hematopoietic stem cells	blood
34	chr12:117477400-117481400	Enhancers	Stomach Mucosa	stomach
35	chr12:117477400-117482800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr12:117477400-117482800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:117477400-117483000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr12:117477400-117484800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr12:117477600-117478000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:117477600-117478000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr12:117477600-117478200	Enhancers	Brain Anterior Caudate	brain
42	chr12:117477600-117478600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
43	chr12:117477600-117478800	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr12:117477600-117480200	Weak transcription	HSMMtube	muscle
45	chr12:117477600-117482800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr12:117477800-117478200	Weak transcription	K562	blood
47	chr12:117477800-117478800	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr12:117477800-117478800	Enhancers	Fetal Thymus	thymus
49	chr12:117477800-117479800	Weak transcription	Gastric	stomach
50	chr12:117477800-117482800	Weak transcription	Fetal Brain Female	brain

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