Variant report

Variant	rs9860910
Chromosome Location	chr3:180014181-180014182
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:180007103..180009299-chr3:180013025..180015189,2	K562	blood:
2	chr3:180002525..180004570-chr3:180012107..180014551,2	MCF-7	breast:
3	chr3:180012187..180014713-chr3:180016610..180018256,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10755138	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12108143	0.83[EUR][1000 genomes]
rs12108145	0.87[EUR][1000 genomes]
rs12486206	0.85[ASN][1000 genomes]
rs12491089	0.87[ASN][1000 genomes]
rs12638851	0.83[ASN][1000 genomes]
rs12638877	0.87[ASN][1000 genomes]
rs1520613	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16831406	0.87[ASN][1000 genomes]
rs2337368	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2337369	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2878954	0.83[ASN][1000 genomes]
rs3849424	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3849425	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3849426	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3906012	0.87[EUR][1000 genomes]
rs3914867	0.83[ASN][1000 genomes]
rs3914868	0.83[ASN][1000 genomes]
rs3914869	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3914871	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4108253	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4241377	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4568133	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4854907	0.88[EUR][1000 genomes]
rs4854968	0.88[EUR][1000 genomes]
rs4854969	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4854970	0.83[ASN][1000 genomes]
rs55996463	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62292326	0.86[ASN][1000 genomes]
rs6769259	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6780998	0.88[EUR][1000 genomes]
rs7622865	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7639931	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7643438	0.84[EUR][1000 genomes]
rs7644566	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7652473	0.84[EUR][1000 genomes]
rs9290697	0.90[CEU][hapmap]
rs939440	0.80[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs939441	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs939442	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9682110	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9683358	0.86[ASN][1000 genomes]
rs9815922	0.88[EUR][1000 genomes]
rs9815923	0.88[EUR][1000 genomes]
rs9818172	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9824544	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9845934	0.90[CEU][hapmap]
rs9864534	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867767	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9869873	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012271	chr3:179806875-180234871	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv878040	chr3:179823887-180128288	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv997388	chr3:179899279-180172349	Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv536817	chr3:179899279-180172349	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv878041	chr3:179983857-180097855	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9860910	IGF2BP2	cis	parietal	SCAN
rs9860910	CAMK2N2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:180013600-180014200	Enhancers	HMEC	breast
2	chr3:180013600-180014600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:180013800-180015800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:180013800-180016400	Weak transcription	Pancreas	Pancrea
5	chr3:180014000-180015600	Enhancers	Adipose Nuclei	Adipose

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