Variant report

Variant	rs17461429
Chromosome Location	chr12:40552895-40552896
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10784340	0.86[CEU][hapmap]
rs10877913	0.86[CEU][hapmap]
rs10877955	0.86[CEU][hapmap]
rs10877971	0.86[CEU][hapmap]
rs10878123	0.86[CEU][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10878208	0.83[ASN][1000 genomes]
rs11174831	0.86[CEU][hapmap]
rs11174928	0.86[CEU][hapmap]
rs11175102	0.86[CEU][hapmap]
rs11175103	0.86[CEU][hapmap]
rs11175256	0.86[CEU][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11175260	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11175332	0.92[ASN][1000 genomes]
rs11175371	0.93[ASN][1000 genomes]
rs11175401	0.86[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11175405	0.85[ASN][1000 genomes]
rs11175422	0.86[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11175458	0.94[ASN][1000 genomes]
rs11175540	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12372213	0.86[CEU][hapmap]
rs12581285	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1388593	0.83[ASN][1000 genomes]
rs1491922	0.83[ASN][1000 genomes]
rs1491923	0.83[ASN][1000 genomes]
rs1491924	0.86[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1491925	0.85[ASN][1000 genomes]
rs17442157	0.86[CEU][hapmap]
rs17443199	0.93[ASN][1000 genomes]
rs17458613	0.85[CEU][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17518546	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1907630	0.83[ASN][1000 genomes]
rs1907631	0.83[ASN][1000 genomes]
rs2046931	0.83[ASN][1000 genomes]
rs2172240	0.83[ASN][1000 genomes]
rs2172241	0.83[ASN][1000 genomes]
rs2201144	0.81[ASN][1000 genomes]
rs2253736	0.83[ASN][1000 genomes]
rs2638244	0.83[ASN][1000 genomes]
rs2638247	0.85[ASN][1000 genomes]
rs2638250	0.88[ASN][1000 genomes]
rs2638268	0.83[ASN][1000 genomes]
rs2638269	0.82[ASN][1000 genomes]
rs2638270	0.93[ASN][1000 genomes]
rs2638271	0.83[ASN][1000 genomes]
rs2708426	0.83[ASN][1000 genomes]
rs2708463	0.83[ASN][1000 genomes]
rs2708465	0.86[ASN][1000 genomes]
rs2708478	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2723260	0.83[ASN][1000 genomes]
rs28365179	0.86[CEU][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28365683	0.85[CEU][hapmap]
rs72644819	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7310104	0.83[ASN][1000 genomes]
rs949640	0.86[CEU][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[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:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40547200-40558600	Weak transcription	Liver	Liver
2	chr12:40548800-40553800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr12:40550800-40553000	Enhancers	Pancreatic Islets	Pancreatic Islet
4	chr12:40551000-40553200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr12:40551200-40553200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:40551200-40553200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr12:40551200-40553200	Enhancers	Muscle Satellite Cultured Cells	--
8	chr12:40551200-40553600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:40551600-40553200	Enhancers	Primary B cells from peripheral blood	blood
10	chr12:40551800-40553200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:40551800-40553400	Enhancers	NHEK	skin
12	chr12:40552000-40553000	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr12:40552000-40556200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:40552200-40553000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr12:40552200-40553200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr12:40552200-40553200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
17	chr12:40552200-40553200	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr12:40552200-40553200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:40552200-40553200	Flanking Active TSS	GM12878-XiMat	blood
20	chr12:40552200-40553400	Enhancers	Primary hematopoietic stem cells	blood
21	chr12:40552400-40553000	Enhancers	Adipose Nuclei	Adipose
22	chr12:40552600-40553000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:40552600-40553000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
24	chr12:40552800-40553000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:40552800-40553000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:40552800-40553000	Enhancers	HMEC	breast

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