Variant report

Variant	rs2365389
Chromosome Location	chr3:61236462-61236463
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11130821	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs11130822	0.90[EUR][1000 genomes]
rs11130826	0.93[EUR][1000 genomes]
rs11130828	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11720254	0.90[EUR][1000 genomes]
rs12053817	0.80[EUR][1000 genomes]
rs12492551	0.93[EUR][1000 genomes]
rs13099397	0.85[ASN][1000 genomes]
rs1470035	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs1524019	0.96[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1554599	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs1554601	0.86[JPT][hapmap]
rs17064630	0.90[EUR][1000 genomes]
rs1916800	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs1916801	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs1916802	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1949772	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1980308	0.87[CEU][hapmap];0.91[EUR][1000 genomes]
rs1980309	0.87[CEU][hapmap];0.91[EUR][1000 genomes]
rs1980310	0.87[CEU][hapmap];0.91[EUR][1000 genomes]
rs1980311	0.90[EUR][1000 genomes]
rs34045993	0.83[ASN][1000 genomes]
rs35198002	0.90[EUR][1000 genomes]
rs4296587	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4535219	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4605537	0.92[EUR][1000 genomes]
rs4688352	0.87[EUR][1000 genomes]
rs4688354	0.89[EUR][1000 genomes]
rs4688355	0.90[EUR][1000 genomes]
rs4688379	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61275795	0.80[EUR][1000 genomes]
rs6445197	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6445198	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6445199	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6445200	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6785875	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6787292	0.84[CEU][hapmap];0.90[EUR][1000 genomes]
rs6787313	0.87[EUR][1000 genomes]
rs6809031	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71296711	0.93[EUR][1000 genomes]
rs7641177	0.81[EUR][1000 genomes]
rs7647122	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs815709	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs815710	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs815712	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs815715	0.87[EUR][1000 genomes]
rs815717	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs843812	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs863635	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9831249	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9832387	0.87[EUR][1000 genomes]
rs9832404	0.85[EUR][1000 genomes]
rs9844741	0.91[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9846073	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs9850114	0.93[EUR][1000 genomes]
rs9855716	0.96[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9856859	0.82[EUR][1000 genomes]
rs9859004	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9860681	0.86[EUR][1000 genomes]
rs9875827	0.88[EUR][1000 genomes]
rs9882800	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876866	chr3:61054494-61310328	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv876867	chr3:61054494-61474575	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv432423	chr3:61100255-61606060	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1000378	chr3:61103229-61238089	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv876868	chr3:61145050-61282503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv532626	chr3:61159646-61388418	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1008399	chr3:61176965-61461349	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 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	chr3:61230600-61236800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:61233200-61236600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:61233200-61236600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:61235200-61236600	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr3:61235400-61237000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:61235400-61237400	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr3:61235400-61237800	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr3:61235600-61236600	Enhancers	H1 Cell Line	embryonic stem cell
9	chr3:61235600-61236600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:61235600-61236600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:61235600-61236600	Enhancers	Gastric	stomach
12	chr3:61235600-61237000	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr3:61235600-61237000	Flanking Active TSS	Fetal Thymus	thymus
14	chr3:61235600-61237000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr3:61235600-61237800	Active TSS	H9 Cell Line	embryonic stem cell
16	chr3:61235600-61237800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr3:61235600-61237800	Active TSS	Left Ventricle	heart
18	chr3:61235600-61238000	Active TSS	Colonic Mucosa	Colon
19	chr3:61235600-61238000	Active TSS	A549	lung
20	chr3:61235600-61238200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:61235800-61236600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:61235800-61236600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:61235800-61236600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:61235800-61236600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:61235800-61236600	Flanking Active TSS	Brain Hippocampus Middle	brain
26	chr3:61235800-61236600	Enhancers	Placenta Amnion	Placenta Amnion
27	chr3:61235800-61236800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr3:61235800-61236800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr3:61235800-61236800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr3:61235800-61236800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:61235800-61236800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:61235800-61236800	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr3:61235800-61236800	Flanking Active TSS	Brain Angular Gyrus	brain
34	chr3:61235800-61236800	Flanking Active TSS	Brain Cingulate Gyrus	brain
35	chr3:61235800-61237000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
36	chr3:61235800-61237000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr3:61235800-61237000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
38	chr3:61235800-61237000	Flanking Active TSS	Dnd41	blood
39	chr3:61235800-61237600	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr3:61235800-61237800	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr3:61235800-61237800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:61235800-61238000	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr3:61235800-61238000	Active TSS	Fetal Brain Female	brain
44	chr3:61235800-61238000	Active TSS	Psoas Muscle	Psoas
45	chr3:61236000-61236600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:61236000-61236600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr3:61236000-61236600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr3:61236000-61236600	Flanking Active TSS	Primary T cells from cord blood	blood
49	chr3:61236000-61236600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr3:61236000-61236600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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