Variant report

Variant	rs11564115
Chromosome Location	chr12:40630639-40630640
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10506148	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10878123	1.00[JPT][hapmap]
rs10878208	0.83[JPT][hapmap]
rs11175256	1.00[JPT][hapmap]
rs11175332	0.95[JPT][hapmap]
rs11175371	0.95[JPT][hapmap]
rs11175401	1.00[JPT][hapmap]
rs11175405	0.89[JPT][hapmap]
rs11175422	1.00[JPT][hapmap]
rs11175558	0.95[JPT][hapmap]
rs1388593	0.91[ASN][1000 genomes]
rs1388596	0.90[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs1472117	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1491924	1.00[JPT][hapmap]
rs1491939	0.90[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs1491942	0.81[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs17443199	0.89[JPT][hapmap]
rs17484286	0.81[CHB][hapmap];0.83[ASN][1000 genomes]
rs1817817	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1907630	0.91[ASN][1000 genomes]
rs1907631	0.91[ASN][1000 genomes]
rs1907634	0.94[ASN][1000 genomes]
rs2046931	0.90[JPT][hapmap]
rs2131088	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2172240	0.91[ASN][1000 genomes]
rs2172241	0.91[ASN][1000 genomes]
rs2201144	0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2638244	0.90[JPT][hapmap]
rs2638268	0.90[JPT][hapmap]
rs2638270	0.95[JPT][hapmap]
rs2638271	0.90[JPT][hapmap]
rs2708426	0.91[ASN][1000 genomes]
rs2708436	0.95[ASN][1000 genomes]
rs2708437	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[ASN][1000 genomes]
rs2708438	0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[ASN][1000 genomes]
rs2708441	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2723260	0.91[ASN][1000 genomes]
rs2723268	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2723269	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs28365179	0.94[JPT][hapmap]
rs4473003	0.85[CHB][hapmap];0.83[CHD][hapmap];0.86[ASN][1000 genomes]
rs7134572	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs7310104	0.90[JPT][hapmap]
rs949640	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044685	chr12:40574460-40771612	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1052661	chr12:40603049-40642812	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
3	nsv1045408	chr12:40620554-40664424	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
4	nsv1042967	chr12:40629636-40710319	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	6 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	chr12:40619400-40634600	Weak transcription	Spleen	Spleen
2	chr12:40619400-40644400	Weak transcription	Gastric	stomach
3	chr12:40619600-40636400	Weak transcription	Fetal Muscle Leg	muscle
4	chr12:40619600-40661000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:40619600-40678400	Weak transcription	Right Ventricle	heart
6	chr12:40619800-40658800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr12:40620400-40644200	Weak transcription	Brain Angular Gyrus	brain
8	chr12:40620800-40634800	Weak transcription	Lung	lung
9	chr12:40620800-40634800	Weak transcription	Pancreas	Pancrea
10	chr12:40620800-40644200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:40620800-40648000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr12:40620800-40659200	Weak transcription	Brain Anterior Caudate	brain
13	chr12:40620800-40704200	Weak transcription	Esophagus	oesophagus
14	chr12:40621000-40632000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:40621000-40643800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr12:40621000-40659800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr12:40621000-40661200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr12:40621200-40631800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:40621200-40632000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:40621400-40632400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:40622800-40661000	Weak transcription	Colon Smooth Muscle	Colon
22	chr12:40622800-40708800	Weak transcription	Left Ventricle	heart
23	chr12:40624600-40631200	Weak transcription	A549	lung
24	chr12:40628000-40631400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr12:40628200-40631400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr12:40628400-40632000	Strong transcription	Primary B cells from cord blood	blood
27	chr12:40628800-40631200	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr12:40629200-40633400	Strong transcription	Adipose Nuclei	Adipose
29	chr12:40629200-40635600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr12:40629400-40632200	Strong transcription	Primary B cells from peripheral blood	blood
31	chr12:40629800-40631200	Strong transcription	Liver	Liver
32	chr12:40630000-40632000	Genic enhancers	Primary monocytes fromperipheralblood	blood
33	chr12:40630600-40631400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr12:40630600-40633000	Weak transcription	Aorta	Aorta
35	chr12:40630600-40633000	Weak transcription	Ovary	ovary
36	chr12:40630600-40643600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr12:40630600-40669400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr12:40630600-40686400	Strong transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links