Variant report

Variant	rs2447001
Chromosome Location	chr12:49275701-49275702
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49253798..49263932-chr12:49272568..49285670,39	MCF-7	breast:
2	chr12:49253541..49263542-chr12:49271204..49284916,35	MCF-7	breast:
3	chr12:49275330..49277454-chr12:49281174..49283027,2	MCF-7	breast:
4	chr12:49270319..49273192-chr12:49274654..49277123,3	MCF-7	breast:
5	chr12:49244448..49248825-chr12:49273797..49278851,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172602	Chromatin interaction
ENSG00000174243	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10747556	0.83[CHB][hapmap]
rs10747557	0.81[CHB][hapmap]
rs10783287	0.87[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10875883	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10875885	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs11168773	0.99[ASN][1000 genomes]
rs12369505	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs2446985	0.90[ASN][1000 genomes]
rs2446986	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2446987	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2446999	0.86[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2447000	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2453476	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2926806	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2934998	0.81[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3958875	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4760647	0.92[ASN][1000 genomes]
rs833476	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs833478	0.96[ASN][1000 genomes]
rs833479	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs833483	0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs833484	0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs833820	0.81[EUR][1000 genomes]
rs833821	0.81[EUR][1000 genomes]
rs9788029	0.83[AMR][1000 genomes];0.87[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	nsv469373	chr12:49256792-49285390	Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
2	nsv558832	chr12:49256792-49285390	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
3	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49271400-49278200	Enhancers	Liver	Liver
2	chr12:49273800-49276800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:49274000-49278800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:49274800-49275800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:49275000-49275800	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr12:49275000-49275800	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr12:49275000-49275800	Enhancers	HUVEC	blood vessel
8	chr12:49275000-49278600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:49275200-49276200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
10	chr12:49275200-49278200	Enhancers	Fetal Intestine Large	intestine
11	chr12:49275200-49278200	Enhancers	Fetal Intestine Small	intestine
12	chr12:49275400-49275800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:49275400-49275800	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr12:49275400-49276000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
15	chr12:49275400-49277800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:49275400-49278200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:49275600-49275800	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr12:49275600-49275800	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr12:49275600-49275800	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr12:49275600-49275800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:49275600-49275800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:49275600-49275800	Enhancers	Adipose Nuclei	Adipose
23	chr12:49275600-49275800	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr12:49275600-49275800	Bivalent Enhancer	K562	blood
25	chr12:49275600-49276000	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr12:49275600-49276000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:49275600-49276000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:49275600-49276000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:49275600-49276000	Enhancers	Aorta	Aorta
30	chr12:49275600-49276000	Active TSS	Brain Hippocampus Middle	brain
31	chr12:49275600-49276000	Bivalent Enhancer	Fetal Heart	heart
32	chr12:49275600-49276200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr12:49275600-49276200	Enhancers	Fetal Kidney	kidney
34	chr12:49275600-49276200	Enhancers	Stomach Mucosa	stomach
35	chr12:49275600-49276200	Bivalent Enhancer	HepG2	liver
36	chr12:49275600-49276400	Bivalent Enhancer	NH-A	brain
37	chr12:49275600-49276600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr12:49275600-49276600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:49275600-49276600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:49275600-49276600	Flanking Bivalent TSS/Enh	Osteobl	bone
41	chr12:49275600-49277000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:49275600-49277200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr12:49275600-49277200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:49275600-49277400	Enhancers	Placenta Amnion	Placenta Amnion
45	chr12:49275600-49277600	Bivalent Enhancer	Fetal Muscle Leg	muscle
46	chr12:49275600-49277800	Enhancers	Placenta	Placenta
47	chr12:49275600-49278000	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr12:49275600-49278000	Enhancers	Fetal Lung	lung
49	chr12:49275600-49278000	Enhancers	Lung	lung
50	chr12:49275600-49278000	Enhancers	Pancreas	Pancrea

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