Variant report

Variant	rs2399369
Chromosome Location	chr3:110617220-110617221
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:110617155..110618688-chr3:110622142..110624409,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10511291	0.96[EUR][1000 genomes]
rs10755069	0.92[ASN][1000 genomes]
rs12493974	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1350930	0.90[ASN][1000 genomes]
rs1350932	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1350979	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1381830	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1381833	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1381834	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1381835	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1381836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1462299	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1462308	0.90[ASN][1000 genomes]
rs1462326	0.98[ASN][1000 genomes]
rs1462798	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1462802	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1542513	0.90[ASN][1000 genomes]
rs1599576	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16857350	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16857358	0.94[ASN][1000 genomes]
rs16857373	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16857536	0.96[EUR][1000 genomes]
rs1870926	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2045784	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2169497	0.92[ASN][1000 genomes]
rs2169565	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2219706	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2399364	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2399367	0.83[AFR][1000 genomes]
rs2399368	0.83[AFR][1000 genomes]
rs4682024	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682025	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682027	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4682215	0.83[AFR][1000 genomes]
rs60037602	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6437934	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6763050	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805467	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs72934030	0.96[EUR][1000 genomes]
rs72934034	0.96[EUR][1000 genomes]
rs72934100	0.96[EUR][1000 genomes]
rs72935934	0.96[EUR][1000 genomes]
rs72948740	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72948795	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72948800	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7629008	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7650516	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs768686	0.85[ASN][1000 genomes]
rs936512	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs969940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828260	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9839231	1.00[EUR][1000 genomes]
rs9881407	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9883216	0.96[EUR][1000 genomes];0.90[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	nsv1003106	chr3:110264476-111105943	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1014199	chr3:110293896-110754155	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2762345	chr3:110614389-110668843	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv829674	chr3:110616256-110771049	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:110607800-110619600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:110608200-110618400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:110611400-110628600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:110612600-110635600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:110614200-110621200	Weak transcription	Liver	Liver

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