Variant report

Variant	rs2899006
Chromosome Location	chr4:55307814-55307815
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	chr4:55188891..55189478-chr4:55307244..55307822,2	MCF-7	breast:
2	chr4:55307735..55309712-chr4:55311176..55313685,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251264	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10016644	1.00[EUR][1000 genomes]
rs10032723	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1025931	1.00[EUR][1000 genomes]
rs1025932	1.00[EUR][1000 genomes]
rs1036969	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10746546	1.00[EUR][1000 genomes]
rs11133327	1.00[YRI][hapmap]
rs1156182	1.00[EUR][1000 genomes]
rs11940626	1.00[EUR][1000 genomes]
rs12508708	1.00[EUR][1000 genomes]
rs1354959	1.00[EUR][1000 genomes]
rs1492764	1.00[EUR][1000 genomes]
rs1507960	1.00[EUR][1000 genomes]
rs1507967	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1507969	1.00[EUR][1000 genomes]
rs1507975	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1562057	1.00[EUR][1000 genomes]
rs1867403	1.00[EUR][1000 genomes]
rs1976222	1.00[EUR][1000 genomes]
rs2135969	1.00[EUR][1000 genomes]
rs218272	1.00[EUR][1000 genomes]
rs2412562	1.00[EUR][1000 genomes]
rs2412580	1.00[EUR][1000 genomes]
rs2537877	1.00[EUR][1000 genomes]
rs2703470	1.00[EUR][1000 genomes]
rs2703471	1.00[EUR][1000 genomes]
rs2703482	1.00[EUR][1000 genomes]
rs2703483	1.00[EUR][1000 genomes]
rs2899007	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4864885	1.00[EUR][1000 genomes]
rs4864886	1.00[EUR][1000 genomes]
rs4864888	1.00[EUR][1000 genomes]
rs56744789	1.00[EUR][1000 genomes]
rs59971610	1.00[EUR][1000 genomes]
rs6812224	1.00[EUR][1000 genomes]
rs6841931	1.00[EUR][1000 genomes]
rs6851205	1.00[EUR][1000 genomes]
rs6855353	1.00[EUR][1000 genomes]
rs73148424	1.00[EUR][1000 genomes]
rs73150417	1.00[EUR][1000 genomes]
rs7356494	1.00[EUR][1000 genomes]
rs7661226	1.00[EUR][1000 genomes]
rs925139	1.00[EUR][1000 genomes]
rs931914	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9999573	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008793	chr4:55060925-55535807	Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv537098	chr4:55060925-55535807	Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv999400	chr4:55143598-55776995	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv997430	chr4:55253397-55529288	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55304800-55312200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr4:55307000-55312400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr4:55307200-55309600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr4:55307200-55310400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:55307200-55310800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:55307200-55312200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr4:55307400-55308000	Enhancers	Brain Hippocampus Middle	brain
8	chr4:55307600-55310200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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