Variant report

Variant	rs12490251
Chromosome Location	chr3:47224953-47224954
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12487863	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12490244	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12492463	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493011	0.81[AMR][1000 genomes]
rs12493723	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12495173	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12495438	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17079512	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2291721	0.97[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3733093	0.82[AMR][1000 genomes]
rs3821879	0.81[AMR][1000 genomes]
rs3933020	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4082156	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4627772	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683318	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4683321	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4683323	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58206566	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59601660	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60285825	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7638049	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv590211	chr3:47189485-47256057	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv3801	chr3:47201530-47246438	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1014457	chr3:47222292-47335175	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv536560	chr3:47222292-47335175	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47206800-47228000	Weak transcription	Spleen	Spleen
2	chr3:47207000-47253800	Weak transcription	Aorta	Aorta
3	chr3:47207200-47225800	Weak transcription	Placenta	Placenta
4	chr3:47207200-47235800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:47207800-47228000	Weak transcription	HMEC	breast
6	chr3:47208000-47227800	Weak transcription	K562	blood
7	chr3:47208000-47230600	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:47208000-47249600	Weak transcription	Ovary	ovary
9	chr3:47208200-47225200	Weak transcription	Fetal Intestine Small	intestine
10	chr3:47208200-47225400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:47208200-47229400	Weak transcription	NHLF	lung
12	chr3:47208200-47232600	Weak transcription	Fetal Brain Female	brain
13	chr3:47208200-47256400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:47208200-47276600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:47208400-47225800	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:47217800-47236600	Weak transcription	Right Ventricle	heart
17	chr3:47218200-47226400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:47219400-47243400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:47221000-47250200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:47221400-47236000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:47222400-47228600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:47222600-47225000	Weak transcription	Fetal Lung	lung
23	chr3:47222600-47228600	Weak transcription	HSMM	muscle
24	chr3:47222600-47244200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:47222800-47226600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr3:47222800-47227000	Weak transcription	Fetal Intestine Large	intestine
27	chr3:47222800-47228400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:47222800-47229000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:47222800-47229200	Weak transcription	Brain Angular Gyrus	brain
30	chr3:47222800-47229400	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr3:47222800-47233000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:47222800-47233400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:47222800-47235400	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr3:47222800-47236800	Weak transcription	Left Ventricle	heart
35	chr3:47222800-47249000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr3:47222800-47249400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:47223000-47228000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:47223000-47229600	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr3:47223000-47236400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:47223200-47225800	Weak transcription	Stomach Smooth Muscle	stomach
41	chr3:47223200-47235200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:47223200-47240200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:47223400-47225200	Weak transcription	HSMMtube	muscle
44	chr3:47223400-47233400	Weak transcription	Brain Anterior Caudate	brain
45	chr3:47223400-47242800	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr3:47223400-47245200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:47223400-47256600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr3:47223600-47227400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr3:47223800-47231800	Weak transcription	Fetal Stomach	stomach
50	chr3:47223800-47233000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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