Variant report

Variant	rs11564117
Chromosome Location	chr12:40551564-40551565
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10506143	0.86[AMR][1000 genomes]
rs10506144	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10506146	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10506147	1.00[AFR][1000 genomes]
rs11175186	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11175593	1.00[AFR][1000 genomes]
rs11564107	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11564108	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11564131	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11564190	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11564199	0.83[AMR][1000 genomes]
rs11564212	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11564214	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11564216	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11564218	0.86[AMR][1000 genomes]
rs12422544	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12424040	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12424294	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12425561	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12425630	0.81[AMR][1000 genomes]
rs12426378	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12426643	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12427022	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1388585	1.00[ASN][1000 genomes]
rs1388597	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1491945	0.88[AMR][1000 genomes]
rs17458549	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17458808	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17461387	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17461575	1.00[AFR][1000 genomes]
rs17465610	1.00[AFR][1000 genomes]
rs17483919	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17484003	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17484141	0.82[AMR][1000 genomes]
rs2131081	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2638223	0.93[ASN][1000 genomes]
rs2708460	0.93[ASN][1000 genomes]
rs28365169	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28365173	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28365206	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs28365689	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28370602	1.00[AFR][1000 genomes]
rs28370606	1.00[AFR][1000 genomes]
rs28740171	1.00[AFR][1000 genomes]
rs4767962	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4767964	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4768213	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs535458	1.00[AFR][1000 genomes]
rs545385	1.00[AFR][1000 genomes]
rs549790	1.00[AFR][1000 genomes]
rs729215	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]

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	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv899030	chr12:40509341-40580440	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv899031	chr12:40520684-40580440	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1045516	chr12:40543200-40589557	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40547200-40558600	Weak transcription	Liver	Liver
2	chr12:40547600-40551800	Weak transcription	NHEK	skin
3	chr12:40547800-40551800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:40547800-40552200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:40548800-40553800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:40549600-40552200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr12:40549800-40551600	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr12:40550400-40551600	Weak transcription	Primary B cells from peripheral blood	blood
9	chr12:40550600-40552800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:40550800-40553000	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr12:40551000-40553200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr12:40551200-40551600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr12:40551200-40552000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:40551200-40552600	Enhancers	HMEC	breast
15	chr12:40551200-40553200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:40551200-40553200	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr12:40551200-40553200	Enhancers	Muscle Satellite Cultured Cells	--
18	chr12:40551200-40553600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:40551400-40552000	Enhancers	Primary B cells from cord blood	blood

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