Variant report

Variant	rs897880
Chromosome Location	chr12:10774817-10774818
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:10766930..10769742-chr12:10774668..10777182,2	MCF-7	breast:
2	chr12:10771877..10773786-chr12:10773916..10777458,3	K562	blood:
3	chr12:10770221..10774557-chr12:10774772..10778392,5	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10083164	0.83[JPT][hapmap]
rs1026442	1.00[JPT][hapmap]
rs10431297	0.82[JPT][hapmap]
rs1054396	1.00[JPT][hapmap]
rs1073305	0.82[JPT][hapmap]
rs10743911	0.96[CEU][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10772334	1.00[JPT][hapmap]
rs10772340	0.82[JPT][hapmap]
rs10772343	0.81[JPT][hapmap]
rs10772347	0.82[JPT][hapmap]
rs10845180	0.83[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs10845181	0.82[JPT][hapmap]
rs10845184	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10845185	0.92[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10845192	0.82[JPT][hapmap]
rs10845194	0.81[JPT][hapmap]
rs10845195	0.82[JPT][hapmap]
rs10845197	0.80[JPT][hapmap]
rs10845198	0.82[JPT][hapmap]
rs11053877	1.00[JPT][hapmap]
rs11053880	0.84[GIH][hapmap];1.00[JPT][hapmap]
rs11053881	0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11053882	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12306757	0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12306815	0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12811247	1.00[JPT][hapmap]
rs1870194	0.88[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2125091	0.94[JPT][hapmap]
rs2219382	0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2290718	1.00[JPT][hapmap]
rs2305853	1.00[JPT][hapmap]
rs2418087	0.82[JPT][hapmap]
rs2418088	0.82[JPT][hapmap]
rs2900513	0.82[JPT][hapmap]
rs3759264	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3759265	0.87[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs3782674	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6488316	0.82[JPT][hapmap]
rs7312261	0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7313620	0.81[JPT][hapmap]
rs7350557	0.82[JPT][hapmap]
rs7350597	0.82[JPT][hapmap]
rs755498	0.96[ASN][1000 genomes]
rs7968284	0.82[JPT][hapmap]
rs7971142	0.82[JPT][hapmap]
rs897882	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9988929	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832329	chr12:10677094-10845946	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs897880	TAS2R43	cis	parietal	SCAN
rs897880	TAS2R43	cis	cerebellum	SCAN
rs897880	TAS2R13	cis	parietal	SCAN
rs897880	NECAP1	cis	parietal	SCAN
rs897880	STYK1	cis	lung	GTEx
rs897880	HEBP1	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10766600-10787000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:10766600-10789400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:10766600-10794400	Weak transcription	Gastric	stomach
4	chr12:10766800-10789400	Weak transcription	Esophagus	oesophagus
5	chr12:10767000-10778400	Weak transcription	Colonic Mucosa	Colon
6	chr12:10767200-10775000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr12:10767200-10780600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr12:10767200-10781200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:10767600-10776800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr12:10770600-10777600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr12:10771200-10776000	Strong transcription	Rectal Mucosa Donor 31	rectum
12	chr12:10771400-10782200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:10771600-10775800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:10771800-10775400	Strong transcription	HUVEC	blood vessel
15	chr12:10771800-10775600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:10772000-10775200	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr12:10772000-10775400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr12:10772000-10787200	Weak transcription	NHEK	skin
19	chr12:10772400-10775800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:10772400-10780600	Weak transcription	HMEC	breast
21	chr12:10773000-10775200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:10773000-10777200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr12:10773000-10780200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr12:10773000-10786600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr12:10773000-10787000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:10773200-10776600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:10773400-10787000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:10774000-10775000	Enhancers	HSMM	muscle
29	chr12:10774600-10777800	Enhancers	NHDF-Ad	bronchial
30	chr12:10774600-10784000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr12:10774600-10784400	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links