Variant report

Variant	rs2270794
Chromosome Location	chr12:117477104-117477105
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:117477087..117480724-chr12:117486826..117489814,3	MCF-7	breast:
2	chr12:117470652..117475607-chr12:117477009..117480553,6	K562	blood:
3	chr12:117469991..117472353-chr12:117476644..117478230,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10507277	0.83[EUR][1000 genomes]
rs10507278	0.86[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs10735099	0.81[CEU][hapmap]
rs10735102	0.81[CEU][hapmap]
rs10735103	0.81[EUR][1000 genomes]
rs10850733	0.85[ASN][1000 genomes]
rs10850741	0.94[ASN][1000 genomes]
rs10850743	0.81[CEU][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs11068264	0.81[CEU][hapmap]
rs11068277	0.81[CEU][hapmap]
rs11068296	0.81[CEU][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs11838192	0.94[ASN][1000 genomes]
rs12299065	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12302906	0.94[ASN][1000 genomes]
rs16947275	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs16947281	0.83[EUR][1000 genomes]
rs2173653	1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2242469	0.85[EUR][1000 genomes]
rs2393111	0.80[TSI][hapmap]
rs3782193	0.88[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3893370	0.83[TSI][hapmap]
rs4076700	0.80[TSI][hapmap]
rs4238051	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4542506	0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs4562927	0.81[CEU][hapmap]
rs4766815	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs4766821	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs4767473	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4767474	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs4767483	0.80[TSI][hapmap]
rs4767484	0.81[CEU][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs4767485	0.81[EUR][1000 genomes]
rs4767487	0.82[EUR][1000 genomes]
rs4767489	0.81[CEU][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs4767490	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4767491	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs4767493	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs59348125	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60940473	0.94[ASN][1000 genomes]
rs6490101	1.00[JPT][hapmap]
rs7137006	0.81[CEU][hapmap]
rs7137752	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs7297155	0.82[EUR][1000 genomes]
rs7297848	0.81[CEU][hapmap]
rs7302025	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7305948	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7307907	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7308498	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs7316144	0.82[EUR][1000 genomes]
rs73403241	0.87[EUR][1000 genomes]
rs73405256	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73405273	0.83[ASN][1000 genomes]
rs7954600	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957907	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7958030	0.81[EUR][1000 genomes]
rs7959666	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs7960610	1.00[JPT][hapmap]
rs7962339	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973240	0.80[TSI][hapmap]
rs7973925	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977598	0.82[EUR][1000 genomes]
rs7978725	0.89[ASN][1000 genomes]
rs7979277	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308	0.81[GIH][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9804817	1.00[CHB][hapmap];1.00[JPT][hapmap];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
rs2270794	TESC	cis	parietal	SCAN

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	chr12:117466600-117479800	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	chr12:117468600-117477400	Weak transcription	Primary B cells from cord blood	blood
7	chr12:117470800-117483400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr12:117471200-117482800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr12:117471400-117479800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:117471600-117480200	Weak transcription	Esophagus	oesophagus
11	chr12:117471600-117482600	Weak transcription	Primary B cells from peripheral blood	blood
12	chr12:117471800-117477200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr12:117471800-117477400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr12:117472000-117482600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:117472200-117477200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr12:117472200-117477400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr12:117472200-117478400	Weak transcription	Primary T cells from cord blood	blood
18	chr12:117472200-117479800	Weak transcription	Right Atrium	heart
19	chr12:117472600-117480200	Weak transcription	Ovary	ovary
20	chr12:117472600-117483000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr12:117473000-117477600	Weak transcription	K562	blood
22	chr12:117473400-117478400	Weak transcription	Brain Germinal Matrix	brain
23	chr12:117473800-117477600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:117474000-117479800	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr12:117474400-117478400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr12:117474600-117477600	Weak transcription	Fetal Brain Female	brain
27	chr12:117474600-117479600	Weak transcription	Fetal Heart	heart
28	chr12:117474600-117479600	Weak transcription	Spleen	Spleen
29	chr12:117474800-117479600	Weak transcription	Left Ventricle	heart
30	chr12:117475000-117477200	Strong transcription	A549	lung
31	chr12:117476000-117478200	Strong transcription	Pancreas	Pancrea
32	chr12:117476000-117479600	Weak transcription	Fetal Intestine Large	intestine
33	chr12:117476000-117479600	Weak transcription	Fetal Intestine Small	intestine
34	chr12:117476200-117477600	Weak transcription	Brain Anterior Caudate	brain
35	chr12:117476200-117477600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr12:117476400-117477400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr12:117476400-117479800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:117476400-117484600	Weak transcription	Dnd41	blood
39	chr12:117476600-117477600	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr12:117476600-117479800	Weak transcription	Right Ventricle	heart
41	chr12:117476800-117477400	Weak transcription	Stomach Mucosa	stomach
42	chr12:117476800-117478000	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr12:117476800-117478200	Strong transcription	HepG2	liver
44	chr12:117477000-117477200	Enhancers	Fetal Stomach	stomach
45	chr12:117477000-117477400	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr12:117477000-117477400	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr12:117477000-117477600	Enhancers	H1 Cell Line	embryonic stem cell
48	chr12:117477000-117477800	Strong transcription	Gastric	stomach
49	chr12:117477000-117478200	Enhancers	Brain Inferior Temporal Lobe	brain

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