Variant report

Variant	rs12486248
Chromosome Location	chr3:47082774-47082775
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47082604..47084164-chr3:47087207..47088724,2	K562	blood:
2	chr3:47081998..47084579-chr3:47088555..47090930,2	K562	blood:

Variant related genes	Relation type
ENSG00000181555	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12485582	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12487863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12489851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12491419	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12493723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12497141	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17079425	1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2305632	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2305640	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35201996	0.94[ASN][1000 genomes]
rs3816531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4082156	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4683276	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4683318	0.81[AMR][1000 genomes]
rs4683321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs59601660	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs60285825	0.94[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs61364027	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7372834	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

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	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	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
5	nsv997261	chr3:47054766-47133680	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47061200-47083000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:47069600-47088200	Strong transcription	Liver	Liver
3	chr3:47069600-47088200	Strong transcription	Fetal Intestine Large	intestine
4	chr3:47069600-47089000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:47069800-47086600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:47070400-47089000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:47073400-47087600	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr3:47073600-47087800	Strong transcription	Fetal Muscle Leg	muscle
9	chr3:47073600-47088200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:47073800-47082800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:47073800-47083200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:47073800-47088200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:47074200-47086600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:47074200-47086800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:47074400-47088600	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr3:47074600-47084200	Strong transcription	Fetal Muscle Trunk	muscle
17	chr3:47074600-47084400	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr3:47074600-47085400	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:47074600-47086600	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:47074600-47088200	Strong transcription	NH-A	brain
21	chr3:47074600-47088400	Strong transcription	Placenta	Placenta
22	chr3:47074800-47088800	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr3:47075400-47088200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr3:47075600-47088200	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:47075800-47085000	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:47075800-47086600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:47076000-47084200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:47076000-47085000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:47077000-47084200	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr3:47078000-47130600	Weak transcription	Stomach Mucosa	stomach
31	chr3:47078200-47084200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:47078400-47085800	Strong transcription	Fetal Stomach	stomach
33	chr3:47078800-47101400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr3:47079000-47083000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
35	chr3:47079000-47084800	Strong transcription	Fetal Lung	lung
36	chr3:47079400-47083800	Strong transcription	Fetal Intestine Small	intestine
37	chr3:47079400-47088400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:47079400-47088800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:47079400-47095800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:47079600-47085400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr3:47079600-47088400	Weak transcription	Fetal Heart	heart
42	chr3:47079600-47088600	Weak transcription	Brain Substantia Nigra	brain
43	chr3:47079600-47088800	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr3:47079600-47123800	Weak transcription	Pancreas	Pancrea
45	chr3:47079600-47124200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:47079800-47095000	Weak transcription	HMEC	breast
47	chr3:47079800-47098000	Weak transcription	Aorta	Aorta
48	chr3:47079800-47124200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr3:47080000-47095200	Weak transcription	Fetal Brain Male	brain
50	chr3:47080400-47087000	Strong transcription	Primary B cells from peripheral blood	blood

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