Variant report

Variant	rs10169629
Chromosome Location	chr2:48625044-48625045
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48620898..48623309-chr2:48624782..48626327,2	K562	blood:
2	chr2:48617829..48620871-chr2:48622412..48626412,3	K562	blood:

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10153773	0.82[JPT][hapmap]
rs10199431	0.83[JPT][hapmap]
rs10208627	0.88[ASN][1000 genomes]
rs10495951	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs10495952	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11676168	0.86[JPT][hapmap]
rs11679523	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11680719	0.83[JPT][hapmap];0.91[EUR][1000 genomes]
rs11680916	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11682633	0.87[ASN][1000 genomes]
rs11683099	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11683639	0.82[JPT][hapmap]
rs11685861	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs11686007	0.81[ASN][1000 genomes]
rs11688481	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs11689622	0.82[JPT][hapmap]
rs11689645	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11690690	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11690748	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11690845	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs12052754	0.90[ASN][1000 genomes]
rs12105983	0.88[ASN][1000 genomes]
rs12328506	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13388291	0.81[JPT][hapmap]
rs13398791	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13401749	0.82[JPT][hapmap]
rs13432998	0.82[JPT][hapmap]
rs17037289	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs17037298	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs17855177	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4316980	0.82[JPT][hapmap]
rs4344965	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs4411759	0.82[JPT][hapmap]
rs4547570	0.99[ASN][1000 genomes]
rs4641990	0.87[JPT][hapmap]
rs4953572	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs55660911	0.92[ASN][1000 genomes]
rs55744465	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55761545	0.86[ASN][1000 genomes]
rs56156294	0.94[ASN][1000 genomes]
rs56163539	0.83[ASN][1000 genomes]
rs56365822	0.85[ASN][1000 genomes]
rs56391806	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57131168	0.81[ASN][1000 genomes]
rs57537506	0.91[ASN][1000 genomes]
rs57893565	0.94[ASN][1000 genomes]
rs58012056	0.93[ASN][1000 genomes]
rs58978223	0.84[ASN][1000 genomes]
rs59045263	0.88[ASN][1000 genomes]
rs60042255	0.85[ASN][1000 genomes]
rs60825643	1.00[ASN][1000 genomes]
rs61303367	0.85[ASN][1000 genomes]
rs62137015	0.93[ASN][1000 genomes]
rs62137018	0.92[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs62137019	0.86[ASN][1000 genomes]
rs62137021	0.84[ASN][1000 genomes]
rs6545030	0.87[JPT][hapmap]
rs6545036	0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs66705539	0.87[ASN][1000 genomes]
rs6705802	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6712029	0.86[JPT][hapmap]
rs6718068	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6722246	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6735288	0.88[ASN][1000 genomes]
rs6743757	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6745580	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6747441	0.85[ASN][1000 genomes]
rs6749773	0.85[ASN][1000 genomes]
rs6756596	0.97[ASN][1000 genomes]
rs72818502	0.84[ASN][1000 genomes]
rs72820403	0.88[ASN][1000 genomes]
rs72820404	0.90[ASN][1000 genomes]
rs72820409	0.90[ASN][1000 genomes]
rs72820411	0.90[ASN][1000 genomes]
rs72820415	0.90[ASN][1000 genomes]
rs72820416	0.90[ASN][1000 genomes]
rs72820418	0.90[ASN][1000 genomes]
rs72820420	0.91[ASN][1000 genomes]
rs72820422	0.92[ASN][1000 genomes]
rs72820423	0.93[ASN][1000 genomes]
rs72820424	0.90[ASN][1000 genomes]
rs72820427	0.93[ASN][1000 genomes]
rs72820433	0.92[ASN][1000 genomes]
rs72820436	0.92[ASN][1000 genomes]
rs72820437	0.94[ASN][1000 genomes]
rs72820439	0.94[ASN][1000 genomes]
rs72820441	0.90[ASN][1000 genomes]
rs72820445	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72820454	0.85[ASN][1000 genomes]
rs7559431	0.89[ASN][1000 genomes]
rs7562069	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7562816	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7566239	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7568574	0.86[ASN][1000 genomes]
rs7573316	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7576964	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7577237	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7579932	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7600794	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7606104	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[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	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv581775	chr2:48619869-48714938	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv518718	chr2:48624007-48650308	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10169629	PPP1R21	cis	Thyroid	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48619400-48625400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr2:48623200-48625600	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr2:48623600-48625400	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr2:48623600-48626800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr2:48623600-48626800	Weak transcription	Fetal Intestine Large	intestine
6	chr2:48623600-48626800	Weak transcription	Fetal Intestine Small	intestine
7	chr2:48623800-48626600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:48624400-48626200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:48624400-48626200	Enhancers	Fetal Lung	lung
10	chr2:48624600-48625200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:48624600-48626000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:48624600-48626000	Enhancers	Adipose Nuclei	Adipose
13	chr2:48624600-48626000	Enhancers	Fetal Heart	heart
14	chr2:48624600-48627800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr2:48624800-48625200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:48624800-48626400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr2:48625000-48625200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:48625000-48625200	Flanking Active TSS	Brain Anterior Caudate	brain
19	chr2:48625000-48625200	Flanking Active TSS	Brain Cingulate Gyrus	brain
20	chr2:48625000-48625200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
21	chr2:48625000-48625400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:48625000-48625400	Active TSS	Brain Germinal Matrix	brain
23	chr2:48625000-48625400	Enhancers	K562	blood
24	chr2:48625000-48625600	Active TSS	Brain Angular Gyrus	brain
25	chr2:48625000-48625800	Active TSS	Brain Hippocampus Middle	brain
26	chr2:48625000-48625800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr2:48625000-48625800	Active TSS	Brain Substantia Nigra	brain
28	chr2:48625000-48625800	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr2:48625000-48626000	Flanking Active TSS	Fetal Brain Male	brain
30	chr2:48625000-48626000	Active TSS	Fetal Brain Female	brain

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