Variant report

Variant	rs11065003
Chromosome Location	chr12:120479682-120479683
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:120479228..120480776-chr12:120492305..120495211,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255575	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10128766	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10400498	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10400560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849731	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10849732	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs10849735	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs10849736	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11064987	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11064988	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11064996	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11833221	0.91[ASN][1000 genomes]
rs12310269	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12310591	1.00[ASN][1000 genomes]
rs12311327	0.82[CHB][hapmap]
rs12313413	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12318774	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12320793	0.92[ASN][1000 genomes]
rs12322236	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12422923	1.00[ASN][1000 genomes]
rs16949901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16949946	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.87[YRI][hapmap];0.88[ASN][1000 genomes]
rs16949961	0.91[ASN][1000 genomes]
rs17841967	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2239200	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.92[ASN][1000 genomes]
rs2239201	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.92[ASN][1000 genomes]
rs2239202	0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2239203	0.92[ASN][1000 genomes]
rs2239204	0.91[ASN][1000 genomes]
rs2283359	0.89[ASN][1000 genomes]
rs2283360	0.90[ASN][1000 genomes]
rs2286040	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28726166	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2893812	0.83[CHB][hapmap]
rs3742042	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3742044	0.83[CHB][hapmap]
rs3886910	0.83[CHB][hapmap]
rs4105713	0.85[ASN][1000 genomes]
rs4767869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4767871	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767872	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767875	1.00[ASN][1000 genomes]
rs4767876	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58272825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59168361	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60466490	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490278	0.83[CHB][hapmap]
rs6490281	0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs7298183	0.94[ASN][1000 genomes]
rs7298727	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7300023	0.86[ASW][hapmap];0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.91[ASN][1000 genomes]
rs7302874	0.83[CHB][hapmap]
rs7304325	0.83[CHB][hapmap]
rs7312811	0.83[CHB][hapmap]
rs7312971	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7397339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956436	0.82[CHB][hapmap]
rs7958402	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7958497	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.93[MEX][hapmap];0.87[ASN][1000 genomes]
rs7960725	0.83[CHB][hapmap]
rs7962812	0.83[CHB][hapmap]
rs7965829	1.00[ASW][hapmap];0.87[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7968557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977281	0.83[CHB][hapmap]
rs7978927	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv899554	chr12:120389613-120513625	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120454200-120484800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr12:120477600-120479800	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr12:120478000-120480200	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr12:120478200-120480000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:120478200-120480200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr12:120478400-120480000	Enhancers	Primary T cells fromperipheralblood	blood
7	chr12:120478600-120479800	Enhancers	H9 Cell Line	embryonic stem cell
8	chr12:120478600-120479800	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr12:120478600-120480400	Enhancers	Stomach Mucosa	stomach
10	chr12:120478800-120480000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:120478800-120480000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr12:120479000-120479800	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr12:120479000-120479800	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr12:120479000-120479800	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr12:120479000-120480200	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr12:120479200-120479800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:120479200-120479800	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr12:120479200-120479800	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr12:120479200-120479800	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr12:120479200-120479800	Enhancers	Liver	Liver
21	chr12:120479200-120479800	Enhancers	NHEK	skin
22	chr12:120479200-120480000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:120479200-120480000	Enhancers	Brain Cingulate Gyrus	brain
24	chr12:120479200-120480000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr12:120479200-120480000	Enhancers	Pancreas	Pancrea
26	chr12:120479200-120481200	Enhancers	HMEC	breast
27	chr12:120479200-120481400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:120479200-120481600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:120479200-120481600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:120479400-120479800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:120479400-120479800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:120479400-120479800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr12:120479400-120479800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:120479400-120480000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr12:120479400-120480200	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr12:120479600-120480000	Genic enhancers	Primary T cells from cord blood	blood
37	chr12:120479600-120480200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr12:120479600-120481600	Enhancers	HepG2	liver

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