Variant report

Variant	rs7068497
Chromosome Location	chr10:89542058-89542059
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:89531576..89533907-chr10:89541046..89543285,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10218936	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10887752	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11202536	0.87[CEU][hapmap]
rs11202538	0.87[CEU][hapmap]
rs11202553	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs11202555	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11202557	0.87[CEU][hapmap];0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs11202564	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11202565	0.82[AMR][1000 genomes]
rs11202571	0.87[CEU][hapmap]
rs11816798	0.87[CEU][hapmap];0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs11817759	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs11818430	0.81[EUR][1000 genomes]
rs12247482	0.81[EUR][1000 genomes]
rs12253113	0.87[CEU][hapmap];0.80[MEX][hapmap]
rs12570639	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs12573160	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs12573349	0.81[EUR][1000 genomes]
rs12762731	0.87[CEU][hapmap];0.80[MEX][hapmap]
rs12770684	0.81[EUR][1000 genomes]
rs12771188	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs12772552	0.87[CEU][hapmap]
rs12773536	0.87[CEU][hapmap]
rs12775017	0.87[CEU][hapmap];0.80[MEX][hapmap]
rs12775041	0.87[CEU][hapmap]
rs12778199	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs12779915	0.87[CEU][hapmap]
rs12780237	0.87[CEU][hapmap];0.80[MEX][hapmap]
rs12781171	0.87[CEU][hapmap];0.80[MEX][hapmap]
rs12782235	0.81[EUR][1000 genomes]
rs12783598	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs1321934	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1819162	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs1819163	0.81[EUR][1000 genomes]
rs1853167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1923260	0.81[EUR][1000 genomes]
rs1923261	0.81[EUR][1000 genomes]
rs1923262	0.81[EUR][1000 genomes]
rs1993845	0.87[CEU][hapmap];0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs2038554	0.83[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs2057358	0.87[CEU][hapmap]
rs3781189	0.87[YRI][hapmap]
rs3816651	0.87[CEU][hapmap]
rs6586102	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs7085412	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7090088	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs7098653	0.82[EUR][1000 genomes]
rs7481	0.83[CEU][hapmap]
rs7898915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7904344	0.87[CEU][hapmap];0.85[TSI][hapmap]
rs7908641	0.82[EUR][1000 genomes]
rs7910692	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs7920778	0.87[CEU][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap]
rs9651491	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs9663978	0.81[EUR][1000 genomes]
rs9664653	0.87[CEU][hapmap];0.80[MEX][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518233	chr10:89512839-89584002	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1041462	chr10:89518729-89584284	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7068497	LIPJ	cis	cerebellum	SCAN
rs7068497	PAPSS2	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:89473000-89577200	Weak transcription	Gastric	stomach
2	chr10:89476200-89542400	Weak transcription	Pancreas	Pancrea
3	chr10:89495000-89576400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr10:89495200-89542600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr10:89495200-89544600	Weak transcription	Brain Substantia Nigra	brain
6	chr10:89495200-89559200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr10:89495200-89577400	Weak transcription	Spleen	Spleen
8	chr10:89504200-89551800	Weak transcription	Psoas Muscle	Psoas
9	chr10:89507000-89557600	Weak transcription	Lung	lung
10	chr10:89510200-89553800	Weak transcription	Esophagus	oesophagus
11	chr10:89511000-89576800	Weak transcription	Colonic Mucosa	Colon
12	chr10:89512800-89560400	Weak transcription	Fetal Brain Male	brain
13	chr10:89513400-89577000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr10:89516400-89557800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr10:89518200-89556600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr10:89518400-89559000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr10:89520200-89542800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr10:89520400-89556400	Weak transcription	Brain Germinal Matrix	brain
19	chr10:89520600-89575600	Weak transcription	Stomach Mucosa	stomach
20	chr10:89523200-89553000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr10:89523400-89562800	Weak transcription	K562	blood
22	chr10:89523800-89562000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr10:89524600-89560400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr10:89526000-89549000	Weak transcription	Brain Angular Gyrus	brain
25	chr10:89526200-89549400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr10:89527400-89542600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr10:89527400-89553600	Weak transcription	Colon Smooth Muscle	Colon
28	chr10:89527400-89575000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr10:89527600-89554000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr10:89527600-89554200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr10:89527800-89547800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr10:89529600-89542600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr10:89529600-89542800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr10:89530800-89549800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr10:89530800-89575800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr10:89533200-89545000	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr10:89533400-89545000	Strong transcription	Dnd41	blood
38	chr10:89533600-89545000	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr10:89534000-89544800	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr10:89534800-89542200	Weak transcription	Placenta	Placenta
41	chr10:89535400-89545200	Strong transcription	Primary B cells from peripheral blood	blood
42	chr10:89536200-89544400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr10:89536200-89557800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr10:89536200-89574600	Weak transcription	Brain Anterior Caudate	brain
45	chr10:89536400-89542400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr10:89536400-89549000	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr10:89536600-89543200	Strong transcription	A549	lung
48	chr10:89536600-89544600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr10:89536600-89551000	Weak transcription	NHLF	lung
50	chr10:89537000-89560400	Weak transcription	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links