Variant report

Variant	rs12104490
Chromosome Location	chr2:172083452-172083453
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172081700..172084390-chr2:172085144..172088000,3	MCF-7	breast:
2	chr2:172082247..172084518-chr2:172109275..172110941,2	MCF-7	breast:
3	chr2:172016384..172019023-chr2:172081901..172083621,2	K562	blood:
4	chr2:172074108..172075791-chr2:172081448..172083975,2	K562	blood:

Variant related genes	Relation type
ENSG00000198586	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10168737	0.85[ASN][1000 genomes]
rs10169565	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10179563	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10179755	0.85[ASN][1000 genomes]
rs10188041	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10193428	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10200190	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10203429	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10203448	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12475659	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12476502	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13382841	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13391119	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13391878	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13413830	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13420362	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13420513	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13420514	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13423781	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13430050	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16859221	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28510750	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28648794	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28695385	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28761317	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28804212	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28822687	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58470363	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61553554	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172077200-172083600	Weak transcription	Placenta	Placenta
2	chr2:172081200-172084000	Enhancers	HMEC	breast
3	chr2:172081200-172084400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:172081400-172084400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:172081600-172084000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:172082000-172084400	Enhancers	NHEK	skin
7	chr2:172082400-172083600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr2:172082400-172083600	Weak transcription	Osteobl	bone
9	chr2:172082400-172083800	Weak transcription	K562	blood
10	chr2:172082600-172083600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:172083400-172083600	Weak transcription	GM12878-XiMat	blood
12	chr2:172083400-172084000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:172083400-172084000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:172083400-172086000	Weak transcription	HSMMtube	muscle
15	chr2:172083400-172086200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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