Variant report

Variant	rs11169105
Chromosome Location	chr12:39078755-39078756
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	chr12:39078731..39079461-chr2:68493058..68493608,2	MCF-7	breast:

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1095573	0.84[AFR][1000 genomes]
rs1095576	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11168929	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11169037	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11169056	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11169268	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11169324	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11559976	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12231800	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1486342	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1486343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1486355	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1523119	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1523120	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1533918	0.84[AFR][1000 genomes]
rs1615648	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1621487	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1684397	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1684405	0.82[AMR][1000 genomes]
rs1719833	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs1719847	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1996879	0.84[AFR][1000 genomes]
rs2069210	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2134398	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2455609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2455610	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2630776	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2630778	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2630780	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2630782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2653722	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2653738	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2653752	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2653754	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2653760	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2653761	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2653769	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2653775	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2730897	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2730901	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2730908	0.80[AMR][1000 genomes]
rs2730944	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2730946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2730948	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2730949	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2730954	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2730955	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2730957	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2730964	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4494337	0.81[EUR][1000 genomes]
rs60368384	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60539249	0.86[AFR][1000 genomes]
rs68075931	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73269131	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8181763	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8181765	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs826839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs826840	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs826841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs826845	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs826846	0.88[AMR][1000 genomes]
rs826847	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs826849	0.94[AMR][1000 genomes]
rs826853	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs826854	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs826857	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs826860	0.87[AMR][1000 genomes]
rs826861	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs826862	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs826863	0.82[AMR][1000 genomes]
rs826866	0.82[AMR][1000 genomes]
rs826867	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs826868	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs826869	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs826871	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs826872	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs826880	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs826887	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs826890	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs826894	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs826895	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs826896	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs851933	0.86[AMR][1000 genomes]
rs862331	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs862332	0.97[AMR][1000 genomes]
rs866120	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469356	chr12:38242029-39187408	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv558574	chr12:38242029-39187408	Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv1039538	chr12:38640895-39180750	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1039821	chr12:38959645-39121578	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1053316	chr12:38959645-39122853	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv1043831	chr12:38979065-39117868	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv541479	chr12:38979065-39117868	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv1045040	chr12:39038114-39084094	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
9	esv3333662	chr12:39075385-39079683	ZNF genes & repeats Strong transcription Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39046000-39085400	Weak transcription	Aorta	Aorta
2	chr12:39046800-39080400	Weak transcription	Spleen	Spleen
3	chr12:39051600-39080400	Weak transcription	Lung	lung
4	chr12:39051600-39080800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:39055800-39100800	Weak transcription	NHEK	skin
6	chr12:39056000-39080200	Weak transcription	Ovary	ovary
7	chr12:39056000-39092200	Weak transcription	Colon Smooth Muscle	Colon
8	chr12:39056000-39114800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:39056000-39168600	Weak transcription	Hela-S3	cervix
10	chr12:39056200-39079000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr12:39056200-39080200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr12:39056800-39083000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:39057400-39083000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:39058200-39079000	Weak transcription	GM12878-XiMat	blood
15	chr12:39061200-39080400	Weak transcription	A549	lung
16	chr12:39061600-39080200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr12:39063800-39080400	Weak transcription	Fetal Intestine Large	intestine
18	chr12:39063800-39082600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:39066200-39114400	Weak transcription	Pancreas	Pancrea
20	chr12:39066600-39083400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:39069000-39079000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr12:39069000-39080400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr12:39069400-39114600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr12:39069800-39083000	Weak transcription	Left Ventricle	heart
25	chr12:39071600-39079200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:39074400-39098800	Weak transcription	Right Ventricle	heart
27	chr12:39075200-39080000	Weak transcription	Fetal Intestine Small	intestine
28	chr12:39075400-39080400	Strong transcription	Liver	Liver
29	chr12:39075800-39081200	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr12:39077000-39079800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:39077800-39080800	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr12:39078000-39079200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr12:39078200-39080400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:39078400-39079400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr12:39078400-39079400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr12:39078400-39080200	Strong transcription	Adipose Nuclei	Adipose
37	chr12:39078600-39079400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links