Variant report

Variant	rs66805489
Chromosome Location	chr3:105121812-105121813
allele	CA/TG
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10049426	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1036582	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10511243	0.88[AFR][1000 genomes]
rs10933816	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10933817	0.87[AFR][1000 genomes]
rs12488994	0.90[AFR][1000 genomes]
rs12491980	0.90[AFR][1000 genomes]
rs12494392	0.88[AFR][1000 genomes]
rs12695118	0.88[AFR][1000 genomes]
rs13062366	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs13092811	0.87[AFR][1000 genomes]
rs13093663	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13097669	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs13100098	0.91[AFR][1000 genomes]
rs1438538	0.89[AFR][1000 genomes]
rs1438541	0.87[AFR][1000 genomes]
rs1530069	0.91[AFR][1000 genomes]
rs1898654	0.88[AFR][1000 genomes]
rs2164956	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2178407	0.90[AFR][1000 genomes]
rs2196745	0.90[AFR][1000 genomes]
rs2399045	0.91[AFR][1000 genomes]
rs28670976	0.81[EUR][1000 genomes]
rs2895299	0.91[AFR][1000 genomes]
rs4426702	0.90[AFR][1000 genomes]
rs4894831	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs57834585	0.86[EUR][1000 genomes]
rs6437587	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6437589	0.86[EUR][1000 genomes]
rs6767277	0.91[AFR][1000 genomes]
rs6767814	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6769302	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6779807	0.91[AFR][1000 genomes]
rs6780238	0.90[AFR][1000 genomes]
rs6806304	0.90[AFR][1000 genomes]
rs7615005	0.90[AFR][1000 genomes]
rs7629589	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7644273	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7649033	0.85[AFR][1000 genomes]
rs9288802	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9288805	0.83[AFR][1000 genomes]
rs934856	0.91[AFR][1000 genomes]
rs9842028	0.86[EUR][1000 genomes]
rs9851952	0.87[AFR][1000 genomes]
rs9883620	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9883799	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105113400-105122400	Weak transcription	Primary B cells from cord blood	blood
2	chr3:105114600-105123400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr3:105115800-105122200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:105118400-105122200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:105118600-105122000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr3:105119000-105122000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:105119000-105122200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:105119000-105123000	Weak transcription	Liver	Liver
9	chr3:105119000-105133600	Weak transcription	Brain Angular Gyrus	brain
10	chr3:105119200-105123200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:105120000-105130000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:105120200-105122600	ZNF genes & repeats	GM12878-XiMat	blood
13	chr3:105120400-105129400	Weak transcription	Brain Anterior Caudate	brain
14	chr3:105120600-105122000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:105120800-105122400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:105121000-105122000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:105121000-105122600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:105121000-105134800	Weak transcription	NHLF	lung
19	chr3:105121200-105122000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
20	chr3:105121200-105122000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:105121200-105122200	Active TSS	A549	lung
22	chr3:105121200-105122200	Weak transcription	HSMMtube	muscle
23	chr3:105121200-105122400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:105121200-105122400	ZNF genes & repeats	Fetal Intestine Small	intestine
25	chr3:105121200-105122400	ZNF genes & repeats	Fetal Stomach	stomach
26	chr3:105121200-105122400	ZNF genes & repeats	Lung	lung
27	chr3:105121200-105122600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:105121200-105124000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:105121200-105128600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr3:105121200-105130200	Weak transcription	Brain Hippocampus Middle	brain
31	chr3:105121400-105122000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr3:105121400-105122600	Enhancers	HMEC	breast
33	chr3:105121400-105124600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:105121600-105122000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:105121600-105122000	Weak transcription	Pancreas	Pancrea
36	chr3:105121600-105122200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:105121600-105122400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:105121600-105122400	Strong transcription	Osteobl	bone
39	chr3:105121600-105124000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:105121600-105136600	Weak transcription	HSMM	muscle
41	chr3:105121800-105122000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:105121800-105122000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:105121800-105122000	Weak transcription	Gastric	stomach
44	chr3:105121800-105122000	Weak transcription	NHEK	skin
45	chr3:105121800-105122200	Weak transcription	Aorta	Aorta
46	chr3:105121800-105122400	Enhancers	Hela-S3	cervix
47	chr3:105121800-105122800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr3:105121800-105133600	Weak transcription	NH-A	brain
49	chr3:105121800-105133800	Weak transcription	Muscle Satellite Cultured Cells	--

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