Variant report

Variant	rs72820420
Chromosome Location	chr2:48577103-48577104
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10169629	0.91[ASN][1000 genomes]
rs10208627	0.83[ASN][1000 genomes]
rs10495951	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10495952	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11676036	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11678403	0.83[AFR][1000 genomes]
rs11679523	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11680916	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11682633	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11683099	0.91[ASN][1000 genomes]
rs11684517	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11685861	0.96[ASN][1000 genomes]
rs11686007	0.87[ASN][1000 genomes]
rs11687708	0.84[ASN][1000 genomes]
rs11688481	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11689645	0.90[ASN][1000 genomes]
rs11690690	0.96[ASN][1000 genomes]
rs11690748	0.96[ASN][1000 genomes]
rs11690845	0.80[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12052754	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12105983	0.83[ASN][1000 genomes]
rs12328506	0.92[ASN][1000 genomes]
rs13398791	0.92[ASN][1000 genomes]
rs17037289	0.93[ASN][1000 genomes]
rs17037298	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17855177	0.96[ASN][1000 genomes]
rs4344965	0.95[ASN][1000 genomes]
rs4547570	0.92[ASN][1000 genomes]
rs55660911	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55744465	0.89[ASN][1000 genomes]
rs55761545	0.93[ASN][1000 genomes]
rs55788229	0.83[ASN][1000 genomes]
rs56156294	0.89[ASN][1000 genomes]
rs56163539	0.86[ASN][1000 genomes]
rs56365822	0.81[ASN][1000 genomes]
rs56391806	0.89[ASN][1000 genomes]
rs57131168	0.86[ASN][1000 genomes]
rs57537506	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57893565	0.94[ASN][1000 genomes]
rs58012056	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs59045263	0.83[ASN][1000 genomes]
rs59697023	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60042255	0.81[ASN][1000 genomes]
rs60815228	0.85[ASN][1000 genomes]
rs60825643	0.91[ASN][1000 genomes]
rs61303367	0.81[ASN][1000 genomes]
rs62137001	0.82[AFR][1000 genomes]
rs62137005	0.88[AFR][1000 genomes]
rs62137015	0.95[ASN][1000 genomes]
rs62137019	0.81[ASN][1000 genomes]
rs6545036	0.85[ASN][1000 genomes]
rs66705539	0.83[ASN][1000 genomes]
rs6705802	0.96[ASN][1000 genomes]
rs6718068	0.96[ASN][1000 genomes]
rs6722246	0.96[ASN][1000 genomes]
rs6735288	0.83[ASN][1000 genomes]
rs6743757	0.94[ASN][1000 genomes]
rs6745580	1.00[ASN][1000 genomes]
rs6749773	0.81[ASN][1000 genomes]
rs6756596	0.93[ASN][1000 genomes]
rs72818488	0.86[ASN][1000 genomes]
rs72818491	0.84[ASN][1000 genomes]
rs72818494	0.84[ASN][1000 genomes]
rs72818502	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72820403	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72820404	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72820409	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72820411	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72820415	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72820416	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72820418	0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs72820422	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72820423	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72820424	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72820427	0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs72820433	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72820436	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72820437	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72820439	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72820441	0.92[ASN][1000 genomes]
rs72820445	0.96[ASN][1000 genomes]
rs72820454	0.81[ASN][1000 genomes]
rs7559431	0.90[ASN][1000 genomes]
rs7562069	0.96[ASN][1000 genomes]
rs7562816	0.92[ASN][1000 genomes]
rs7566239	0.94[ASN][1000 genomes]
rs7568574	0.82[ASN][1000 genomes]
rs7573316	0.96[ASN][1000 genomes]
rs7576964	0.96[ASN][1000 genomes]
rs7577237	0.96[ASN][1000 genomes]
rs7579932	0.96[ASN][1000 genomes]
rs7600794	0.92[ASN][1000 genomes]
rs7606104	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv874001	chr2:48534363-48624007	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv874002	chr2:48547751-48610367	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
4	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
5	nsv874003	chr2:48570509-48619869	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48569000-48580000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr2:48570800-48577400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:48571200-48605200	Weak transcription	Colonic Mucosa	Colon
4	chr2:48571600-48580000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:48572200-48597000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr2:48572400-48580000	Weak transcription	Stomach Mucosa	stomach
7	chr2:48573000-48578000	ZNF genes & repeats	GM12878-XiMat	blood
8	chr2:48573200-48577600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr2:48573200-48577800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
10	chr2:48573200-48578400	ZNF genes & repeats	Primary B cells from cord blood	blood
11	chr2:48573200-48578800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:48573200-48579400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
13	chr2:48573400-48578000	ZNF genes & repeats	Fetal Intestine Large	intestine
14	chr2:48573400-48578000	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr2:48573400-48578400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
16	chr2:48573400-48578800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
17	chr2:48573400-48579200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:48573400-48579200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:48573400-48583200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:48573600-48578600	Weak transcription	Pancreas	Pancrea
21	chr2:48573600-48579000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:48573600-48579200	ZNF genes & repeats	A549	lung
23	chr2:48573600-48579400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:48573600-48579400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
25	chr2:48573600-48604000	Weak transcription	Ovary	ovary
26	chr2:48573800-48577200	Weak transcription	Right Atrium	heart
27	chr2:48573800-48577600	Weak transcription	Right Ventricle	heart
28	chr2:48574000-48577600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:48574000-48578800	Weak transcription	HUVEC	blood vessel
30	chr2:48574200-48577800	Strong transcription	Osteobl	bone
31	chr2:48574200-48578000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:48574200-48581000	Genic enhancers	HepG2	liver
33	chr2:48574200-48602000	Weak transcription	Gastric	stomach
34	chr2:48574400-48577600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:48574400-48578200	Strong transcription	HSMM	muscle
36	chr2:48574400-48578600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:48574600-48602000	Weak transcription	Small Intestine	intestine
38	chr2:48574800-48577200	Weak transcription	Brain Cingulate Gyrus	brain
39	chr2:48574800-48578000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr2:48574800-48578200	Strong transcription	Fetal Thymus	thymus
41	chr2:48574800-48589600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr2:48574800-48589600	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr2:48575200-48578200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:48575600-48577800	ZNF genes & repeats	Fetal Kidney	kidney
45	chr2:48575600-48578000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:48575800-48577600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:48575800-48577600	ZNF genes & repeats	Thymus	Thymus
48	chr2:48575800-48577800	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr2:48575800-48579000	ZNF genes & repeats	Fetal Intestine Small	intestine
50	chr2:48576000-48577200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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