Variant report

Variant	rs2802562
Chromosome Location	chr1:224950129-224950130
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	chr1:224949023..224950840-chr1:224954199..224956791,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225334	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10495228	0.83[LWK][hapmap]
rs12567091	0.87[YRI][hapmap]
rs1436166	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs16858661	0.87[YRI][hapmap]
rs16858758	0.83[LWK][hapmap];0.87[YRI][hapmap]
rs16858831	1.00[YRI][hapmap]
rs1961688	0.87[YRI][hapmap]
rs2005073	0.87[YRI][hapmap]
rs2016652	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2501078	0.82[JPT][hapmap]
rs2574874	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2574876	0.86[ASN][1000 genomes]
rs2574877	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2574878	0.83[AMR][1000 genomes]
rs2574879	0.83[ASN][1000 genomes]
rs2662906	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2662907	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2662923	0.83[ASN][1000 genomes]
rs2662924	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2662925	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2662927	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2802552	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2802556	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2802558	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2802559	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2802561	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2802563	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2802730	0.81[AMR][1000 genomes]
rs2802744	0.86[ASN][1000 genomes]
rs2802747	0.83[AMR][1000 genomes]
rs2997478	0.88[ASN][1000 genomes]
rs2997499	0.89[AMR][1000 genomes]
rs2997501	0.88[ASN][1000 genomes]
rs3012182	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3012183	0.81[AMR][1000 genomes]
rs3012184	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv524125	chr1:224902054-225021860	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224944800-224954800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:224947200-224950400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:224947200-224951400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:224948000-224956800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:224949600-224951200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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