Variant report

Variant	rs2708453
Chromosome Location	chr12:40478652-40478653
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:40476970..40478917-chr12:40480066..40482046,2	MCF-7	breast:
2	chr12:40468895..40470933-chr12:40476626..40479292,2	K562	blood:
3	chr12:40478482..40480663-chr12:40481421..40484352,2	MCF-7	breast:
4	chr12:40468130..40470395-chr12:40476626..40479537,2	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1384234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1384236	0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1463718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1482289	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491933	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17458501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1994090	1.00[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs2708446	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768212	0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7134524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304279	0.83[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306944	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315459	0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7978715	0.97[ASN][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	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv899028	chr12:40478652-40524180	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv899029	chr12:40478652-40536061	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40453800-40487400	Weak transcription	Left Ventricle	heart
2	chr12:40464400-40493200	Weak transcription	Colon Smooth Muscle	Colon
3	chr12:40466400-40498200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:40471400-40496800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr12:40474400-40497000	Weak transcription	Ovary	ovary
6	chr12:40474800-40480600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr12:40475400-40483000	Weak transcription	Adipose Nuclei	Adipose
8	chr12:40475400-40497200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr12:40475600-40496400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:40475800-40479400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:40475800-40480000	Weak transcription	Right Ventricle	heart
12	chr12:40476000-40479400	Weak transcription	Liver	Liver
13	chr12:40476000-40480200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:40476200-40485400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr12:40476400-40486200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr12:40476400-40492400	Weak transcription	K562	blood
17	chr12:40476400-40497400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:40476600-40480400	Weak transcription	Aorta	Aorta
19	chr12:40476600-40484600	Weak transcription	Fetal Intestine Large	intestine
20	chr12:40476600-40492600	Weak transcription	Lung	lung
21	chr12:40476600-40498400	Weak transcription	Fetal Stomach	stomach
22	chr12:40476800-40479000	Weak transcription	Fetal Intestine Small	intestine
23	chr12:40476800-40480400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:40476800-40480600	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr12:40476800-40481400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:40476800-40497800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:40477000-40480600	Weak transcription	HepG2	liver
28	chr12:40477000-40492000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr12:40477000-40497000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr12:40477200-40495200	Weak transcription	Hela-S3	cervix
31	chr12:40477400-40481800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:40477400-40496800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr12:40478600-40492600	Weak transcription	Rectal Mucosa Donor 29	rectum

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