Variant report

Variant	rs12909220
Chromosome Location	chr15:50162274-50162275
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	chr15:50160465..50162892-chr15:50168093..50170147,2	K562	blood:

Variant related genes	Relation type
ENSG00000104043	Chromatin interaction

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

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

rs_ID	r²[population]
rs11070732	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11635372	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12594650	0.96[CEU][hapmap];0.81[JPT][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12902281	0.96[CEU][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes]
rs12909948	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16962955	0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs16962997	0.91[JPT][hapmap]
rs16963010	0.85[JPT][hapmap]
rs28369666	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28391660	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs34760149	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4414432	0.95[JPT][hapmap]
rs57169939	0.81[ASN][1000 genomes]
rs60020506	0.85[ASN][1000 genomes]
rs61347161	0.85[ASN][1000 genomes]
rs6493382	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71394987	0.92[EUR][1000 genomes]
rs7178500	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7180532	0.85[ASN][1000 genomes]
rs7181711	0.81[ASN][1000 genomes]
rs755067	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8028196	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8030539	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8034348	0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.84[ASN][1000 genomes]
rs8042949	0.82[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	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv833003	chr15:50100372-50273309	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50135200-50181400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:50135800-50187400	Weak transcription	Liver	Liver
3	chr15:50138200-50189800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr15:50145600-50200400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr15:50149400-50198000	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr15:50156000-50168400	Weak transcription	Ovary	ovary
7	chr15:50158400-50167800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:50158800-50163600	Weak transcription	Adipose Nuclei	Adipose
9	chr15:50158800-50170600	Weak transcription	Placenta	Placenta
10	chr15:50159200-50168400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr15:50159800-50163000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr15:50160600-50162400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr15:50160600-50168600	Weak transcription	Hela-S3	cervix
14	chr15:50160800-50163600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:50161000-50163200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:50161200-50163600	Weak transcription	Osteobl	bone
17	chr15:50161400-50163200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr15:50161600-50175600	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr15:50161800-50179000	Strong transcription	Primary hematopoietic stem cells	blood
20	chr15:50161800-50210600	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr15:50162200-50164600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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