Variant report

Variant	rs3910072
Chromosome Location	chr3:156560926-156560927
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156559469..156561892-chr3:156564883..156566469,2	K562	blood:
2	chr3:156554023..156556645-chr3:156558836..156560959,2	MCF-7	breast:
3	chr3:156536226..156539045-chr3:156559314..156561294,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10936038	0.81[EUR][1000 genomes]
rs10936043	0.82[ASN][1000 genomes]
rs11707914	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11709901	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11711674	0.80[EUR][1000 genomes]
rs11712111	0.89[ASN][1000 genomes]
rs12492968	0.83[EUR][1000 genomes]
rs12629380	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12634915	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12638253	0.89[ASN][1000 genomes]
rs13070271	0.83[ASN][1000 genomes]
rs13097325	0.80[EUR][1000 genomes]
rs13322318	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1384538	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1560415	0.81[EUR][1000 genomes]
rs1560416	0.81[EUR][1000 genomes]
rs17382070	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2060015	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2321290	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2321292	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2321455	0.84[ASN][1000 genomes]
rs2874488	0.81[ASN][1000 genomes]
rs2874495	0.82[ASN][1000 genomes]
rs344079	0.80[ASN][1000 genomes]
rs344080	0.80[ASN][1000 genomes]
rs344082	0.80[ASN][1000 genomes]
rs344084	0.81[ASN][1000 genomes]
rs344087	0.85[ASN][1000 genomes]
rs34667021	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs416600	0.80[ASN][1000 genomes]
rs453219	0.83[ASN][1000 genomes]
rs4589888	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4680312	0.89[ASN][1000 genomes]
rs62275765	0.82[ASN][1000 genomes]
rs6765353	0.81[ASN][1000 genomes]
rs6780427	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7615304	0.82[ASN][1000 genomes]
rs7637701	0.86[ASN][1000 genomes]
rs7638330	0.81[ASN][1000 genomes]
rs7638625	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812895	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9818684	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9820830	0.81[EUR][1000 genomes]
rs9837038	0.96[ASN][1000 genomes]
rs9837271	0.81[EUR][1000 genomes]
rs9844054	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9847187	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9858158	0.89[ASN][1000 genomes]
rs9865905	0.86[ASN][1000 genomes]
rs9866373	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9867621	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9871817	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9875585	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9875688	0.85[ASN][1000 genomes]
rs9876010	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3910072	LINC00886	cis	Nerve Tibial	GTEx
rs3910072	LINC00886	cis	Artery Tibial	GTEx
rs3910072	LINC00886	cis	Artery Aorta	GTEx
rs3910072	LINC00886	cis	Stomach	GTEx
rs3910072	LINC00886	cis	lung	GTEx
rs3910072	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx
rs3910072	LINC00886	cis	Adipose Subcutaneous	GTEx
rs3910072	LINC00886	cis	Esophagus Muscularis	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156554400-156561000	Weak transcription	Aorta	Aorta
2	chr3:156557200-156561000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:156559400-156561600	Enhancers	Fetal Brain Male	brain
4	chr3:156560400-156561000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:156560400-156561000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:156560400-156561000	Enhancers	Osteobl	bone
7	chr3:156560600-156561000	Enhancers	NHDF-Ad	bronchial
8	chr3:156560600-156561200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:156560800-156561000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:156560800-156561000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:156560800-156561200	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr3:156560800-156561600	Enhancers	Muscle Satellite Cultured Cells	--

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