Variant report

Variant	rs6769259
Chromosome Location	chr3:180035013-180035014
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10755138	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12108143	0.81[EUR][1000 genomes]
rs12108145	0.84[EUR][1000 genomes]
rs12486206	0.85[ASN][1000 genomes]
rs12491089	0.86[ASN][1000 genomes]
rs12638851	0.83[ASN][1000 genomes]
rs12638877	0.86[ASN][1000 genomes]
rs1520613	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16831406	0.88[ASN][1000 genomes]
rs2337368	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2337369	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2878951	0.80[AMR][1000 genomes]
rs2878954	0.83[ASN][1000 genomes]
rs3849424	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3849425	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3849426	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3906012	0.83[EUR][1000 genomes]
rs3914867	0.82[ASN][1000 genomes]
rs3914868	0.82[ASN][1000 genomes]
rs3914869	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3914871	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4108253	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4241377	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4568133	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4854907	0.84[EUR][1000 genomes]
rs4854968	0.84[EUR][1000 genomes]
rs4854969	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4854970	0.82[ASN][1000 genomes]
rs55996463	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62292326	0.87[ASN][1000 genomes]
rs6780998	0.84[EUR][1000 genomes]
rs7622865	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7639931	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7643438	0.81[EUR][1000 genomes]
rs7644566	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7652473	0.80[EUR][1000 genomes]
rs9290697	0.86[CEU][hapmap]
rs939440	0.80[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs939441	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs939442	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9682110	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9683358	0.85[ASN][1000 genomes]
rs9815922	0.84[EUR][1000 genomes]
rs9815923	0.84[EUR][1000 genomes]
rs9818172	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9824544	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9845934	0.86[CEU][hapmap]
rs9860910	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9864534	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9867767	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9869873	0.85[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
rs6769259	CAMK2N2	cis	parietal	SCAN
rs6769259	IGF2BP2	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:180024800-180039000	Weak transcription	Ovary	ovary
2	chr3:180030000-180037200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:180030200-180037400	Weak transcription	HMEC	breast
4	chr3:180034200-180035200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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