Variant report

Variant	rs56052407
Chromosome Location	chr3:105194595-105194596
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1020110	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10433369	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10446292	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10511244	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12186012	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12186024	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12491519	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12495149	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12630634	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12633488	0.83[ASN][1000 genomes]
rs12637538	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1347792	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1347793	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1438540	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16844719	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16844723	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16851091	0.83[ASN][1000 genomes]
rs16851172	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16851188	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2007681	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2007688	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2164954	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55639861	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56018019	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60073537	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6437591	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6437592	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6437593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6437594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73177460	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73177480	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73181308	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73183107	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73183124	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73185128	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73185129	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73185131	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73185136	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73185137	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73189029	0.93[ASN][1000 genomes]
rs9637374	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9637375	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9637376	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9637377	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv877304	chr3:105122214-105198374	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105191400-105200600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr3:105192600-105199400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:105193000-105209000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:105193000-105215400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:105193200-105199800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:105193200-105209400	Weak transcription	HSMM	muscle
7	chr3:105193200-105209400	Weak transcription	NH-A	brain
8	chr3:105193200-105213600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:105194000-105199000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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