Variant report

Variant	rs56276589
Chromosome Location	chr3:52772198-52772199
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11510435	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12107484	1.00[EUR][1000 genomes]
rs17052357	1.00[EUR][1000 genomes]
rs17052404	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34173244	1.00[EUR][1000 genomes]
rs4532127	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56134416	1.00[EUR][1000 genomes]
rs56156188	1.00[EUR][1000 genomes]
rs56665533	1.00[EUR][1000 genomes]
rs57008939	1.00[EUR][1000 genomes]
rs57298447	1.00[EUR][1000 genomes]
rs57757646	1.00[EUR][1000 genomes]
rs57789542	1.00[EUR][1000 genomes]
rs57869735	1.00[EUR][1000 genomes]
rs57946083	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58409398	1.00[EUR][1000 genomes]
rs58528592	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58564212	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59638016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59869286	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60040519	1.00[EUR][1000 genomes]
rs60058353	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60256157	1.00[EUR][1000 genomes]
rs60311166	1.00[EUR][1000 genomes]
rs60770874	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60830326	1.00[EUR][1000 genomes]
rs61220667	1.00[EUR][1000 genomes]
rs61538294	1.00[EUR][1000 genomes]
rs6445536	1.00[EUR][1000 genomes]
rs6762788	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6769720	1.00[EUR][1000 genomes]
rs6780005	0.87[EUR][1000 genomes]
rs6780397	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72950424	1.00[EUR][1000 genomes]
rs72950432	1.00[EUR][1000 genomes]
rs72950437	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960212	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960237	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960240	1.00[EUR][1000 genomes]
rs72960260	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960274	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960281	1.00[EUR][1000 genomes]
rs72960285	1.00[EUR][1000 genomes]
rs72965177	1.00[EUR][1000 genomes]
rs72965181	1.00[EUR][1000 genomes]
rs73839126	1.00[EUR][1000 genomes]
rs73839129	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7645785	1.00[EUR][1000 genomes]
rs764636	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7647992	1.00[EUR][1000 genomes]
rs934839	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv508219	chr3:52741193-52803899	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52741600-52804000	Weak transcription	Psoas Muscle	Psoas
2	chr3:52742400-52772800	Weak transcription	Pancreas	Pancrea
3	chr3:52749200-52779800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:52749400-52776200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:52756200-52777400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:52761600-52781000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:52761600-52802400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:52762000-52787000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr3:52762400-52772200	Weak transcription	Thymus	Thymus
10	chr3:52762600-52776000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:52763800-52788400	Strong transcription	Fetal Brain Female	brain
12	chr3:52763800-52802600	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:52764000-52800200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:52764000-52802800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr3:52764200-52774200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:52764400-52776000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr3:52764400-52802600	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:52764800-52781600	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr3:52764800-52789400	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:52765200-52789400	Strong transcription	Adipose Nuclei	Adipose
21	chr3:52765200-52793400	Strong transcription	Fetal Intestine Large	intestine
22	chr3:52765400-52800400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:52765600-52788800	Strong transcription	Brain Anterior Caudate	brain
24	chr3:52765600-52789000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:52765600-52789400	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr3:52766200-52789600	Strong transcription	Placenta	Placenta
27	chr3:52766400-52789400	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr3:52766400-52802600	Strong transcription	Fetal Thymus	thymus
29	chr3:52767000-52785400	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr3:52767200-52788000	Strong transcription	Brain Germinal Matrix	brain
31	chr3:52767600-52775800	Weak transcription	Spleen	Spleen
32	chr3:52767600-52776200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr3:52767600-52802600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:52767600-52803400	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr3:52767800-52774400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr3:52767800-52777000	Strong transcription	Liver	Liver
37	chr3:52767800-52777200	Weak transcription	Esophagus	oesophagus
38	chr3:52767800-52777600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr3:52767800-52779800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr3:52767800-52780200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr3:52767800-52786000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr3:52767800-52793000	Weak transcription	Small Intestine	intestine
43	chr3:52767800-52800600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:52768000-52773400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:52768000-52773400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:52768000-52773800	Weak transcription	HUVEC	blood vessel
47	chr3:52768000-52775200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:52768000-52776000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr3:52768000-52777200	Weak transcription	Right Ventricle	heart
50	chr3:52768000-52777400	Weak transcription	NHLF	lung

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