Variant report

Variant	rs4241377
Chromosome Location	chr3:179985492-179985493
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10513771	0.83[ASN][1000 genomes]
rs10755138	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10937025	0.84[AFR][1000 genomes]
rs11929432	0.84[AFR][1000 genomes]
rs12108143	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12108145	0.96[EUR][1000 genomes]
rs12486206	0.84[ASN][1000 genomes]
rs12491089	0.85[ASN][1000 genomes]
rs12497420	0.92[ASN][1000 genomes]
rs12638851	0.82[ASN][1000 genomes]
rs12638877	0.85[ASN][1000 genomes]
rs13322790	0.86[ASN][1000 genomes]
rs1357904	0.85[ASN][1000 genomes]
rs1464845	0.83[ASN][1000 genomes]
rs1520613	0.82[EUR][1000 genomes]
rs1525276	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1589858	0.89[ASN][1000 genomes]
rs16831288	0.98[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs16831406	0.82[ASN][1000 genomes]
rs2091273	0.90[ASN][1000 genomes]
rs2337368	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2337369	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2878954	0.89[ASN][1000 genomes]
rs28828972	0.81[AFR][1000 genomes]
rs3849424	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3849425	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3849426	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3906012	0.95[EUR][1000 genomes]
rs3906013	0.93[ASN][1000 genomes]
rs3906014	0.92[ASN][1000 genomes]
rs3914867	0.88[ASN][1000 genomes]
rs3914868	0.88[ASN][1000 genomes]
rs3914869	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3914871	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4108253	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4568133	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4854903	0.83[ASN][1000 genomes]
rs4854907	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4854964	0.85[ASN][1000 genomes]
rs4854966	0.83[ASN][1000 genomes]
rs4854968	0.96[EUR][1000 genomes]
rs4854969	0.86[EUR][1000 genomes]
rs4854970	0.81[ASN][1000 genomes]
rs55996463	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56234136	0.83[ASN][1000 genomes]
rs62292283	0.83[ASN][1000 genomes]
rs62292284	0.83[ASN][1000 genomes]
rs62292290	0.83[ASN][1000 genomes]
rs62292291	0.83[ASN][1000 genomes]
rs62292292	0.86[ASN][1000 genomes]
rs62292326	0.85[ASN][1000 genomes]
rs6769259	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6780998	0.96[EUR][1000 genomes]
rs73065331	0.84[AFR][1000 genomes]
rs7622125	0.93[ASN][1000 genomes]
rs7622865	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7639931	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643438	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7644566	0.84[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7647413	0.83[AFR][1000 genomes]
rs7652322	0.85[ASN][1000 genomes]
rs7652473	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9290697	0.90[CEU][hapmap]
rs939440	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs939441	0.91[CEU][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs939442	0.84[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs9682110	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9683358	0.85[ASN][1000 genomes]
rs9815922	0.96[EUR][1000 genomes]
rs9815923	0.96[EUR][1000 genomes]
rs9818172	0.86[EUR][1000 genomes]
rs9819178	0.93[ASN][1000 genomes]
rs9824544	0.87[EUR][1000 genomes]
rs9840477	0.84[ASN][1000 genomes]
rs9840775	0.84[ASN][1000 genomes]
rs9845934	0.90[CEU][hapmap]
rs9860526	0.84[ASN][1000 genomes]
rs9860910	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9864534	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9867767	0.83[ASN][1000 genomes]
rs9869517	0.86[ASN][1000 genomes]
rs9869873	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870444	0.81[AFR][1000 genomes]
rs9871936	0.90[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4241377	SENP2	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179980600-179992400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:179984800-179985800	Flanking Active TSS	GM12878-XiMat	blood
3	chr3:179984800-179986000	Flanking Active TSS	Dnd41	blood
4	chr3:179985200-179985600	Flanking Active TSS	HMEC	breast
5	chr3:179985200-179994800	Weak transcription	Brain Angular Gyrus	brain
6	chr3:179985400-179985600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:179985400-179992600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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