Variant report

Variant	rs12370947
Chromosome Location	chr12:30786569-30786570
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:30784879..30786858-chr12:30788783..30790332,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133704	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10444423	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10743729	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10771745	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771756	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10771757	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10771762	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10771768	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs10843804	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10843813	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10843814	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10843815	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10843816	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10843817	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10843822	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs10843824	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10843833	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs10843834	0.82[EUR][1000 genomes]
rs10843835	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs11051005	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051008	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051010	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11051027	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11051048	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11051050	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs11051053	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs11051061	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs12146709	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12303852	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs12369125	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12579616	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12580645	0.81[AMR][1000 genomes]
rs12581001	0.81[AMR][1000 genomes]
rs12809335	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12809355	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12819059	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12825440	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12826615	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12829890	0.81[AMR][1000 genomes]
rs12830910	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16906678	1.00[YRI][hapmap]
rs2241828	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2278558	0.87[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2289302	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2304630	0.90[JPT][hapmap]
rs28881332	0.83[AMR][1000 genomes]
rs34973510	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs35133495	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36074842	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3933852	0.84[ASN][1000 genomes]
rs4082413	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs4335626	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59177896	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61923728	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6487928	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6487939	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7304221	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7311530	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7314823	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7952744	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7955804	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7957141	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs7962737	0.92[YRI][hapmap]
rs7966063	0.90[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7968828	1.00[YRI][hapmap]
rs7971762	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7971870	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7978343	0.80[CEU][hapmap]
rs7979718	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7980510	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	esv3343291	chr12:30455597-30992837	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12370947	IPO8	cis	multi-tissue	Pritchard
rs12370947	IPO8	cis	Artery Tibial	GTEx
rs12370947	IPO8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:30767000-30844200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:30771000-30812200	Weak transcription	Aorta	Aorta
3	chr12:30771200-30804200	Weak transcription	Fetal Brain Male	brain
4	chr12:30774600-30812000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:30775600-30815400	Weak transcription	Right Ventricle	heart
6	chr12:30775800-30813200	Weak transcription	HMEC	breast
7	chr12:30775800-30815200	Weak transcription	NHEK	skin
8	chr12:30776000-30808400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr12:30776800-30791000	Weak transcription	Psoas Muscle	Psoas
10	chr12:30779200-30812200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:30779400-30796400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr12:30779800-30825000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr12:30780200-30795000	Weak transcription	Fetal Intestine Small	intestine
14	chr12:30780400-30796200	Weak transcription	Hela-S3	cervix
15	chr12:30780600-30788400	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr12:30780800-30792600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:30780800-30793000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr12:30780800-30793000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:30780800-30793200	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr12:30780800-30793200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr12:30780800-30847000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr12:30781000-30787200	Strong transcription	Fetal Intestine Large	intestine
23	chr12:30781000-30792800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr12:30781000-30792800	Strong transcription	Primary T cells from cord blood	blood
25	chr12:30781000-30793000	Strong transcription	Liver	Liver
26	chr12:30781200-30786800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:30781200-30787200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:30781200-30787200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:30781200-30787200	Strong transcription	Rectal Smooth Muscle	rectum
30	chr12:30781200-30787200	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr12:30781200-30790000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:30781200-30790200	Strong transcription	Duodenum Mucosa	Duodenum
33	chr12:30781200-30792800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:30781200-30792800	Strong transcription	Primary B cells from peripheral blood	blood
35	chr12:30781200-30792800	Strong transcription	Adipose Nuclei	Adipose
36	chr12:30781200-30792800	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr12:30781200-30793000	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr12:30781200-30793000	Strong transcription	Fetal Thymus	thymus
39	chr12:30781200-30793200	Strong transcription	Dnd41	blood
40	chr12:30781200-30797600	Strong transcription	Primary B cells from cord blood	blood
41	chr12:30781200-30806600	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr12:30781400-30788200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr12:30781400-30788600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr12:30781400-30793200	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr12:30781600-30787200	Strong transcription	Fetal Brain Female	brain
46	chr12:30781600-30789000	Strong transcription	HUVEC	blood vessel
47	chr12:30781600-30792800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr12:30781600-30793200	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr12:30781800-30788600	Weak transcription	Brain Hippocampus Middle	brain
50	chr12:30781800-30796200	Weak transcription	NHLF	lung

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